Confirmed.
Can max out armor and armor quality and doesn't apply to guns or conning tower.
Also, appears that superstructure armor applies to the conning tower, and conning tower armor doesn't apply to anything.
Furthermore, armor doesn't seem to reset when you goto the shipyard but when you launch the mission according to the tooltips (in mission), not that the armor is there since a 12" turret with 18" of armor gets overpenned by a 4" gun and takes out the whole ship.