Looking at this I think the citadel mechanic along with the barbette mechanic need to go back to the drawing board. It is a manifestation of the same redundancy of mechanics that the shipyard placement scheme suffers: that there are two game functions trying to solve the same problem at the same time and they're getting in each other's way. I think that the citadel armor mechanic should define the how many regions we have to apportion armor to and where in the vessel those regions are. For example the current scheme of deck, belt, their extended variants, turret, and conning tower armor zones is a great start for the the second armor scheme. The first one should at most be hull, deck, turret, and superstructure zones. As the player progresses to new citadel techs like turtle-back and all-or-nothing schemes more regions for armor placement should become available with either an armor viewer like certain MMO naval games or some sort of schematic viewer styled after the historical schematics that lets us see where the armor is relative to our ship's internal components along with some loading screen tips explaining that an all or nothing ship can still be sunk by flooding in the unarmored zones and other such important advice.
For barbettes just make them an armor zone. That and/or maybe rename it to ammo storage scheme or something to define this setting as having to do with the internal structure of the barbette including blast doors, wet ammo storage, and so on.