Armed merchant ships within the Silesian Confederacy
Armed ships are more money. They take more crew. You would have to get some sort of bond with the Mantie government to have that. Training is expensive and missiles are not exactly free.
(1) Prior to the dissolution of the Silesian Confederacy, the Silesian government would not allow armed, civilian-owned merchant vessels even of its own registry (far less anyone else's) to operate in its territorial space. Some of the reasons for that should be clear enough to understand. In a shambles of a star nation where piracy was common, a sizable percentage of those "armed merchantmen" would have ended up turning pirate themselves. That was a significant problem during the periods of our own maritime history in which armed sailing (merchant) ships venturing into risky waters frequently took advantage of their own "defensive" armament to raid anyone else they came across. In Silesia's case, another reason for the dearth of armed merchantships was, frankly, that everybody in a policymaking position — both those who were afraid armed merchies would go rogue and those who were in bed with the existing pirates and smugglers — was opposed to the notion. Those afraid of creating additional pirates were opposed for the reasons given above; those already working with existing pirates were opposed because they didn't want (a) to make it harder for their accomplices to operate or (b) create competition for the aforesaid accomplices. There were some exceptions to the Confederacy's "no guns" rules, but they were few and far between and most of them — the exception would be the fast, armed passenger vessels operated by major shipping lines such as the Hauptman cartel — were technically naval auxiliaries, like Captain Bachfish and his ship.
(2) The primary responsibility for piracy suppression lies with naval units, not self-defending merchant vessels. Self-defense is always a chancy proposition for a merchant ship, as the decision to arm merchant vessels in both world wars demonstrated. Unless you want to turn the merchant vessels into ships which truly are effectively armed naval auxiliaries — like the Hauptman cartel's liners — you're not going to have the crew training and efficiency, the firepower, or the maintenance capability to make your armament effective. There are all sorts of knock-on costs and consequences to effectively arming a merchant vessel, as well. Increases in sensor capability and fire control equipment, for example. Where do you put the weapons — hard points? Pods? "Military-grade" hull segments? What weapons mix do you choose? Energy weapons? In that case you have to let the pirate get to effectively point blank range before you can employ them. Missiles? Depending on the pirate, that could be a good selection or a very, very bad one. When do you show the pirate that you're armed? When he's at long range and might break off without ever attempting to take your vessel? In that case, he gets a good look at your capabilities and if he's big enough and nasty enough, he's not scared off; instead, he knows how to approach you when he closes in. So do you show him that you're armed when he gets to close range, when he won't have time to analyze your weaponry? In that case, he may find himself in a situation where he decides he has no choice but to go all out against your ship because he's matched accelerations and closed to a range at which you can kill him. Generally speaking, the historical experience has been that while arming ships against piratical attack may be good for merchant shipping in general, it's usually not so good for the individual merchant vessels in question. It drives up operating costs for the ships which are armed. It tends to weed out the pirates who can be deterred in the first place, which admittedly reduces the total number of pirates operating in the vicinity, but makes all of the guys who are left substantially more dangerous: more heavily armed, more determined, and more aggressive. And pirates, who are never particularly solicitous about their victims' well-being to begin with, become even less so when they're concerned that those intended victims may actually be able to fight back effectively.
(3) Ports (and star systems) aren't happy about the notion of merchant vessels equipped with the equivalent of two or three eight-inch guns bolted to their hulls turning up in their space. ["I mean, sure, Captain, the port authorities know a good Manticoran skipper like you wouldn't really do something stupid in their harbor with those weapons, but we can't be certain someone else wouldn't. Right? And if we go making an exception to the rules for you, then we have to make it for everybody, don't we?"] For that matter, a lot of the other merchant skippers would sympathize very strongly with those port authorities. And when you think what a couple of impeller drive shipkillers could do to about any planetary target if someone like — oh, I dunno, let's say the Ballroom, for example — was able to get an armed merchantman into the same star system as somebody they didn't like — like, say, a Silesian transstellar doing business with Manpower — things could get messy rather quickly. You don't allow armed vessels into attack range of your facilities, your commerce, or your own population except under extraordinary circumstances, and even then you sweat bullets over the possibility that someone will be stupid enough, careless enough, irate enough, or fanatical enough to actually use that armament against you or someone else.
(4) Merchant vessels are virtually never intercepted in hyper-space; they are intercepted in normal-space after translating out of hyper. The reason piracy prospered in the Silesian Confederacy was that the normal-space volume inside the hyper limit was grossly inadequately controlled/patrolled (in the case of star systems with sufficient population and importance to merit patrols at all) or completely unpatrolled (in the case of "unimportant" star systems where raiders were allowed a free hand). The reason the Royal Manticoran Navy spent so much time patrolling in Silesia was because the Confederacy government wouldn't/couldn't do the patrolling themselves. The Manties were establishing a normal-space presence in the star systems where their commerce was likely to be exposed, and they did it well, prior to the Cold War with Haven. The situation worsened however, after King Roger began a drawdown of the naval strength committed to Silesia — not because he wanted to, but because he needed the funding, the hulls, and the manpower for the buildup against the People's Republic. You can think of it as Jackie Fisher calling home the squadrons the Royal Navy had scattered around the world to concentrate them in Home Fleet to confront the threat of Germany's High Seas Fleet in the North Sea, if you like. (Or the United States downgrading the "Asiatic Fleet" to a cruiser/gunboat level force to concentrate its war-fighting capability as the potential confrontation with Japan heated up in the late 1920s and 1930s.) That created a situation in which Manticoran warships which were still deployed to Silesia faced situations like the ones Honor confronted in "Ms. Midshipwoman Harrington" and "Let's Dance." Now that the Star Empire of Manticore and the Andermani Empire have legal jurisdiction in the star systems of the old Confederacy, there is a permanent, effective, efficient and honest police presence in those normal-space volumes. Most merchant shipping is going to approach the star system on only a handful of (known) vectors, coming in along the ecliptic, and standing patrols are maintained to protect those volumes. Honest merchant skippers know where those volumes (think of them as safe traffic lanes) are, and will deliberately use them on their approach. As a consequence, the opportunity for piracy to occur at all in what used to be the Confederacy has declined drastically, and there is no longer a need/justification for arming merchantships for protection against garden-variety pirates.
(5) There is no point arming merchant vessels to defend themselves against regular warships dispatched on commerce raiding operations, and there are significant arguments against arming them under those circumstances. Unless you're going to build a warship that simply happens to be able to carry some cargo on the side, a cargo carrier is always going to be inferior as a combat platform to a purpose-built warship. Obviously, if you have a 4,000,000-ton freighter and you're willing to sacrifice say 300,000 tons of your total vessel to first-line military systems (and your star nation is willing to let you do that), you can build in the weapons to deter/defeat a 200,000-ton cruiser, at least in theory. However, you have to provide the crew, the training, and the maintenance to use those weapons effectively, and there's nothing to prevent the bad guys from deciding — as they did in the case of Javier Giscard's commerce-raiders in Silesia, for example — from sending battlecruisers instead of light cruisers to do the job. Moreover, under the rules of interstellar warfare, commerce-raiders of a nationstate are required to provide for the personal safety of the crews of any merchant vessels they seize or destroy. However, the merchant vessels in question are required to surrender if their personnel expect the commerce-raiding warship to do that. If the merchie is armed and resists, then any casualties the crew may suffer are fully justified and legal under interstellar law. And on top of that, the reaction of a nation committed to commerce raiding — if its captains know that the merchant traffic they're planning to attack carries significant armament — is going to be to do precisely what the German U-boats did in the Atlantic and the American fleet subs did in the Pacific: assume any merchie they encounter is armed and simply destroy it without exposing themselves any more than absolutely necessary to get the job done. For the U-boats and the fleet subs, that meant torpedoing their targets without warning; in the Honorverse, it would mean blowing them away from maximum missile range.
I don't think it can be too heavily emphasized that it's extraordinarily difficult to find a target anywhere except in normal-space after it reaches its destination or before it crosses the hyper limit of its origination system unless you have implausibly accurate intelligence on the movement schedule of the shipping you're trying to intercept and that shipping — somehow — actually (and miraculously) adheres to that schedule. You have to remember that Honorverse shipping patterns are very, very different from those of our own watery planet's. Oceans are huge, but even so, there are known trade routes and any ship detected by a pirate/raider is subject to attack, capture, or destruction unless it has a sufficient speed advantage to stay out of attack range. That means that convoy and at least some self-defense armament is a practical deterrent to attack. Of course, in a serious commerce war, the actual function of a convoy system is less to deter attack than to invite attack on the defender's terms. In other words, the convoy becomes a tactical defense and a strategic offense against the attacker. However, it doesn't work that way in the Honorverse because vessels in hyper-space are essentially immune from attack/interception. Manticoran warships assigned to convoy duty in the Silesian Confederacy weren't there to protect them in hyper; they were there to provide a moving "bubble" of protected normal-spacein the merchant ships' destination systems. In other words (he said again), they were there to serve as the normal-space anti-piracy patrols the Confederacy didn't provide and which the RMN is providing now that the Confederacy is under new management.
There's definitely some point to armed vessels which are likely to be operating in contested areas. That is, cargo vessels or service vessels which may at least potentially find themselves hypering into a star system they think is safely under their own navy's control only to discover that the other side has taken possession of it, might well find a self-defense armament useful. Fleet auxiliaries — transports, repair ships, missile colliers, etc. — which are likely to be operating in close proximity to naval forces, whether to support an offensive or to provide essential support services in what are supposed to be friendly-controlled star systems in proximity to the zone of combat, always have a valid need for at least minimal self-defense armament. The mere fact that they're going to be operating in proximity to combat vessels in a combat zone means that they may find themselves a lot closer to a battle than they ever wanted to, and the need to deal with any stray shipkillers that come their way — intentionally or accidentally — is always a Good Thing to have. The more likely a non-warship is to find itself conducting actual combat operations, the greater the logic in arming it and the heavier its armament is likely to be. For example, an assault transport is going to be heavily enough armed to look after itself at least against like combatants and, quite probably, to support landing operations against contested targets. But there's no more point in arming a straight supply vessel that happens to belong to the military any more than there would be in arming a civilian supply vessel.
There's a reason Solarian shipping lines routinely don't arm their vessels, and that is that the majority of those vessels call mostly on "civilized" ports. Manticoran merchant vessels are much more likely to find themselves operating somewhere like the old Silesian Confederacy, at which point they require some form of protection. Most effectively, that protection comes from Manticoran warships deployed to patrol and protect the normal-space into which they are going to translate on arrival. If you happened to be transporting a particularly high-value, high-importance cargo — like, say, a ship full of wealthy passengers — it makes sense to go for a belt-and-braces approach "just in case" assuming the local authorities will permit it. Those are unlikely and rather extreme circumstances for the vast majority of merchant vessels, however. What the reader has seen of "the normal state of affairs" in the Silesian Confederacy where Manticoran merchant shipping is concerned is not typical of conditions even in the Silesian Confederacy. It is a situation which did not exist fifty years before Hancock Station, and which got slowly and progressively worse for decades before the war between Manticore and Haven went hot. The Silesian Confederacy was always a risky place for Silesians, because nobody provided special protection for them; until King Roger's build up against Haven began diverting Manticoran strength from its traditional patrol stations in the Confederacy, however, only a lunatic messed with Manticoran merchantships.
I guess what I'm trying to say here is that there is no inherent reason why an effective weapon suite couldn't be integrated into a merchant vessel. The Athena demonstrates one way that could be done, in fact. The problems are that the local government won't approve and that armament isn't needed in areas in which friendly navies control the "local waters" inside and immediately outside the hyper limit of a star system. As a consequence, there's very little reason for a merchant vessel's owner to arm — or even attempt to get permission to arm — his ship.
There will always be some piracy going on in some nook or cranny, just as is happening in the waters off Somalia right now. As in the case of Somalia, however, the instances when that happens are normally going to be the consequence of very area-specific political or societal constraints which preclude anyone from effectively policing those waters. And, of course (as in Somalia's case), there has to be a reason why it's not practical to legally prosecute the pirates under local law or at least for the protecting navies to be unable/unwilling to use military force to burn out the bases from which the pirates operate. If naval captains were still allowed under international law to execute anyone taken in the act of piracy, I strongly suspect that the number of Somalis willing to resort to piracy would plummet steeply.
Silesia was an interstellar Somalia until its division between the Andermani and the Manties. Now it isn't one, and piracy in Silesia is most likely to go back to the way it normally works in places like the Solarian League. You don't use pirate cruisers; you use hijackers. You infiltrate your personnel into the crew or the passenger list of the ship you plan to take, or else you figure out some way to secret your hijackers discreetly in a cargo hold somewhere, and you take the ship from within, timing your attack to occur after it's gone into hyper-space. Then you simply sail it to your chosen destination to loot at your leisure. Obviously, in an operation like that, anti-pirate armament is useless. The safety of your ship depends upon its internal security measures, not whatever weaponry may be bolted to its exterior.