You are significantly underestimating the total amount of semaphore traffic involved. For reasons which I think should be pretty self-evident, since I am writing a series of novels and I'd like to keep at least some uncertainty in the mix, I'm not prepared to offer any sort of definitive numbers of messages and semaphore stations at this time, but part of the problem may be conceptions about exactly how the semaphore system works.
The word "semaphore" conjures up moving arms for most people. The crew at the base of the tower uses cables or rods to position signal arms and so transmit single characters at a time. The Church, however, is an organization -- please remember -- which has controlled an entire planet for the better part of a thousand years, and which has employed semaphore for that entire time. It is a highly sophisticated system, which consists of fairly massive installations on what you might think of as the "main trunk" lines. There are also minor lines, where traffic is relatively light, and which are far less heavily manned and have far smaller transmission capabilities, as a result.
The Church's semaphore should be visualized as an enormous billboard which is lined off into multiple horizontal bands stacked vertically one above another. The individual bands are color-coded, and each of them represents a separate "circuit" in the semaphore chain. Along the length of each band are windows which can be opened and closed and into which removable tiles can be inserted when required. (Many of the "symbol groups" described below can be transmitted simply using patterns of opened and closed windows. In addition, however, specific symbols can be used, and the color coding of the tiles to differentiate between otherwise identical symbols greatly expands the symbols set.) The majority of the traffic is sent using a sophisticated vocabulary which uses numerical/symbol values for whole words, much as the Charisian Navy's signal flags. An enormous percentage of the Church's total message traffic can be transmitted using the three-digit "word codes" rather than spelling out words one letter at a time. (This, by the way, is one reason that the Church's semaphore traffic is scarcely the stuff of brilliantly original composition. The people responsible for sending it are highly trained in using the words actually in the vocabulary in order to squeeze the most bandwidth out of the system, so the Church "officialese" is pretty mindnumbing in a lot of ways by our standards. They can still carry a huge amount of information, but they aren't exactly the kind of readings going to keep you up at night. Messages which are more sophisticated than the semaphore-coding clerks would normally produce are usually sent either overland on horseback or by messenger wyvern, and one should not underestimate the sophistication and size of messages which can be transmitted by wyvern, especially when one considers that the wingspan on the larger messenger wyverns is considerably greater than that of our own largest condors.)
At any rate, each stage in the semaphore system is manned by multiple crews, each of which is responsible for monitoring its own color-coded band and only that color-coded band. Moreover signal discrimination is probably greater than many people are assuming because they aren't taking into consideration the relative sophistication of Safeholdian optics. Please remember that I believe I've had several characters running around wearing glasses, and that even people like Dr. Mahklyn, who requires bifocals, are able to read close work by lamplight, not electrical light. No one has gotten around to the notion of putting two tubes side-by-side to create binoculars, and highly accurate, long-ranged small arms and artillery haven't been around long enough (yet) for anyone to have developed and issued telescopic sights, but the very large, fixed telescopes which are used in the semaphore system give excellent visual resolution at quite extended ranges.
I've always pointed out that the semaphore system is visibility-limited, and that's certainly true, but under normal conditions of visibility (and I am defining "normal" here as those which are normal for the region in which a particular segment of semaphore chain is built), the "repeater stations" are close enough together and equipped with sufficiently capable telescopes to be operable probably somewhere around 75% to 85% of the time under daylight conditions during summer and probably closer to 40% of the time under daylight conditions in the winter. Obviously, in the winter, "daylight conditions" represents a smaller window of each day, so the actual usable transmission time for each day is considerably smaller relative to summer transmission conditions than the simple percentages listed above might seem to suggest. And there are extremely limited night-signaling capabilities, as well. Essentially these consist of using very large and bright reflectors behind the open-and-closed windows of the semaphore board, which means that effectively only single messages can be transmitted at a time and that the symbol set is far more limited. Nonetheless, it is possible to send messages on reasonably clear nights and probably with a higher transmission rate than most readers have been assuming at this point.
Prior to the recent unpleasantness in Charis, the maintenance and extension of the semaphore chain was the single largest infrastructure item on the Church's budget every year. This shouldn't really surprise anyone, since the Church has been aware for centuries of the enormous advantage its ability to manage information faster than anyone else has bestowed upon it. I think I've made that fairly clear in the novels. What they haven't quite tumbled to as yet, because they don't know anything at all about Merlin or his SNARCs, is that their perceived ability to micromanage the situation is actually degrading the effectiveness of their responses at this point. They are so absolutely accustomed to enjoying the shortest command and communication loops of anyone in the world that they don't realize their previously world-beating decision-making loops are no longer anywhere near tight enough to control the situation. But one of the reasons why that sense of superiority is so ingrained is the centuries of effort, thought, and economic resources which have been lavished upon improving the efficiency of their communications system (taken here to mean semaphore, horseback, and wyvern. And, of course, dispatch ship for crossing water gaps).
The Church is also well aware of just how visible the semaphore chain is, and the Church hierarchy is sufficiently accustomed to (and adept at) rivalries and plotting, that truly sensitive messages (defined here as messages whose senders think of them as truly sensitive, which has usually meant messages involved in internal rivalries) which are not absolutely time-critical are generally transmitted either by mounted messenger or by messenger wyvern, where they can't be "overheard" by a trained pair of eyes. At the moment, it hasn't really occurred to any of the Group of Four that their semaphore traffic might be compromised by Charisian agents, since they are operating more or less on the assumption that any "leaks" which occur in the semaphore transmission of messages are occurring because members of the Church's own semaphore service have been bribed by -- or placed in their current positions by -- members of the Church's own hierarchy. In other words, they think that any "taps" on their message traffic are in-house, not put in place by the Church's external enemies (of which there were none of any significance, whatever some members of the Group of Four may have thought, prior to the decision to destroy Charis).
I suppose the points that I'm making here are really twofold. First, the capabilities of the Church's communications systems are very, very much greater than I think most people are assuming in a primarily wind- and muscle-powered society. Second, the sheer volume of traffic, coupled with the alternative means of sending sensitive messages or sending messages in poor visibility conditions, make it much more difficult to comprehensively read the Church's mail than it might originally appear. (And, I suppose, is also a third point, which is that for all its sophistication the system -- and especially its semaphore components -- are very large, very expensive, very fragile, and very vulnerable if any adversary manages to get raiders into position to burn them. Not that I'm suggesting that anyone would possibly be thinking that way. Oh, my, no!)
I should also point out that like bureaucracies everywhere, the Church has discovered that as bandwidth increases, its need for bandwidth increases right along with it. Like bureaucrats throughout human experience, the Church's bureaucrats abhor "dead airspace," and they'll find something to fill it with if it's there. Which, of course, only contributes even more to the sheer bulk of message traffic we're talking about monitoring.
Another point to bear in mind is that Owl is still a very rudimentary AI indeed. I believe I've already commented in another post -- or possibly posts, plural -- that there is a specific reason why he has so little initiative and "imagination." Whatever he may have the potential to grow into someday, he isn't remotely in the same league, far less the same ballpark, as Dahak. He has a lot of growth potential, true, but at the moment it's actually dangerous to rely upon his discretion. He can -- and does -- serve as a first-level filter for a lot of the traffic Merlin is interested in, but at this point even more information is being lost in the filter than Merlin realizes. (Oops! Forget I told you that. It's not supposed to be part of the novels yet. These are not the droids you're looking for. [wavey fingers in front of the nice readers' eyes]) And the fact remains that Merlin has to be the ultimate filter for any and all data collected by his SNARCs. He has to process all of it himself, at least in a supervisory role, then decide what to pass on to someone else and in what kind of format, and he has to do that while simultaneously taking care of all of his other many and manifold responsibilities. And, let us not forget, that whether or not Seijin Merlin has visions, he can afford to let only those cleared for the entire truth about him and about Nimue (which is still a very small group) have any real concept of the total amount of information he can process and distribute. Until, unless, and if Wave Thunder, for example, is cleared for the whole story, Merlin simply cannot [hand] him an outright impossible amount of intelligence information. Remember the scene where he has Owl writing up the take from their intercepts and his thoughts about the volume of what he's reporting.
Merlin Athrawes is both the biggest advantage the Empire of Charis possesses and also the biggest -- or at least most serious -- potential failure point. He has access to information no other kingdom's spymasters could even dream of, but he simply cannot keep his eye on everything happening on the surface of an entire planet. For that matter, he can't even keep up on all of the points he's identified as needing to be kept under observation. Which will have interesting implications when tum-te-tum-te-tum....