First, let's get one thing straight; the splinters which kill people aboard ships in Honor's universe are not from the ships' main armor. They are from internal bulkheads and structural members, and reducing armor would not reduce the danger of splinters when damage penetrates the ship.
All right. Let's start by thinking about what armor in the RMN actually is. It is not battle steel. Battle steel is the alloy from which the main structure of the ship is built. It may be thought of as analagous to present-day steel, but is in fact an advanced composite both lighter and (effectively) denser than steel. It is also harder and tougher--or perhaps the proper word would be elastic--but it is not armor.
What armor is is an advanced sandwich of composites. The outermost skin is a very tough, very hard ceramic "alloy" designed to defeat kinetic as well as energy impacts. It does splinter when hit by something like a graser, but that is allowed for in the design, and it is best thought of as a boundary layer, intended to protect the inner armor system from routine or light damage. Behind the outer skin is a series of sandwiched layers of ablative/refractory armor designed to deflect/absorb/dissipate energy hits. Each sandwich is defined by thin boundaries of the same ceramic which forms the outer skin, and each boundary layer acts, in effect, as splinter armor against anything coming in from the next layer out.
This armor is formed in place once the internal hull is completed. It is, in essence, a "one piece skin" which covers the entire hull, thicker in some places, thinner in others. Its function is not so much to stop all damage from penetrating into the interior of the ship as it is to channel and confine that damage--to limit it, if you will. In addition, the armor itself provides an important aspect of the structural strength of the hull. Remember the pounding that Wayfarer took in Honor Among Enemies? When Ginger Lewis reported to Honor, she expressed her concern about structural integrity--even if Wayfarer had still had operable nodes, Ginger was concerned that her hull had been so ripped and torn that she could not have withstood the stuctural stress of using them. This is one of the things the outer armored skin of a warship is designed to help limit or negate.
Inside the armor comes the hull proper. The outer areas of the hull are not pressurized. This includes the actual weapon bays and most of the passages for as much as fifty to a hundred meters inside the inner edge of the armor. Much of this space (between weapon mounts) is given up to internal bulkheads and a cellular subdivision, once again designed to limit and contain damage. Only the inner core hull--crew quarters, power rooms, etc.--are constantly pressurized. Other portions of the hull--like the "on-mount" crew stations (actually inside separate, heavily protected crew capsules directly adjacent to the weapon mounts) are pressurized between engagements and depressurized once action is imminent. The crews manning those stations put on their skin suits and retain them throughout their time at action stations, which is one reason the RMN insists on standing them down (whenever possible) when it is apparent that action will be joined but not for some hours.
The pressurized core hull is, once again, inside an envelope of armor. This armor consists a series of individual bulkheads separated by gell/liquid barriers to absorb splinters and kinetic energy. Only once that inner armored barrier is passed does one encounter the structural elements which provide the man-killing splinters described in the stories. (The lift shafts are normally pressurized. When cleared for action, a ship depressurizes the shafts, which are sealed at each deck by blast doors. The lift capsules themselves are pressure tight and can move [albeit more slowly] through the blast doors to allow people to get about at action stations. BTW, there are blast doors throughout the ship--indeed, warships are lousy with such emergency bulkheads/doors/barriers. I haven't made a big deal out of their presence because it has always seemed to me that their existence must be self evident.)
There are, of course, chinks in this system. For example, the boat bays represent large, open spaces which are dangerous voids in the outer armored structure, and a "freak" hit in one of these danger areas--like the one which came up through Nike's boat bay at Hancock Station--can penetrate very deep into the core hull despite all the other precautions.
The protective system described above applies to everything down through BCs, although the armor (obviously) gets thinner as the ship gets lighter. Naval designers of Honor's time do not attempt to design ships for combat with their betters; they are intended for combat with their equals or inferiors. Thus a BB's armor scheme would be judged successful if it worked against other BBs, BCs, or lighter units. A DN should be able to stand up to anything of its own size or smaller and to hold its own--at least on a ton-for-ton basis--with an SD. CAs are designed to stand up to other CAs, and to eat CLs and DDs for lunch in close combat, etc.
The RMN (like virtually all other navies) has rejected the notion of armoring its naval personnel's skinsuits. First, a skinsuit is already very tough. It's outer skin is composed of the 41st century equivalent of anti-ballistic fabric. More importantly, please note that there have been references to "storage vacuoles." These are the extremely small cells, located throughout the structure of the skinsuit itself, in which consumables are stored under immense pressure. In effect, each of these small storage "tanks" or vacuoles can be thought of as a small armored bead, which, taken all together, have the effect of producing a sort of chainmail-like, flexible, articulated armor. What the Marines have done is to take this a step further and add additional external armor because they expect their skinnies to stand up to small arms fire. The Navy doesn't expect that. It does expect that its personnel may spend whole days in skinsuits, which makes user comfort, flexibility, and habitability critical factors. The "armor" effect of the vacuoles already offers considerable protection against small splinters, and nothing mobile would properly protect its wearer from the kinetic impact of a battlesteel splinter six to eight feet long and two feet across in its widest dimension traveling at a velocity of a couple of hundred meters-per-second. Also, please bear in mind that while I write about the hits which get through to kill people, whether on weapons mounts or inside the hull, most hits (especially on SDs and DNs) don't get through and kill people. The risk analysis staffs have concluded that the threat of being killed by a largish splinter of the hull is far too small to justify accepting the penalties of heavily armored vac suits. Such suits do exist, but they are intended for construction workers who are likely to get squashed by heavy structural members while building things in space and are rather too bulky and ponderous for movement within a ship.
BTW, there is no point attempting to build armor to protect against "partial compensator failure" because there is no such thing as partial compensator failure. This is one reason running at full military power with no safety margin is so dangerous. The first warning a compensator normally gives of failure is complete breakdown and instant anchovy paste for a crew.