Nuclear Talos may have been stored with the nuclear warhead separately. There's certainly a sperate warhead magazine on the CLG-3 class ships, and IIRC from touring CLG-4 the Talos spaces themselves did not have the security features normal for nuclear weapons, whereas the warhead magazine did.
I can't think of any other weapon that would likely have the warhead stored separately. Terrier, Tomahawk, ASROC, Mk-45 where all integrated weapons only disassembled in shore side facilities. Gravity bombs are nothing but a warhead.
Generally speaking, anything that involves more than cosmetic maintenance on a weapon shipboard is discouraged for any number of reasons. Assembly beyond simple items like installing fins or fitting a seeker (i.e. assembling laser guidance kit to a dumb bomb) is not trivial, and requires significant special tooling, ordinance rated areas, test systems, etc. For instance, the test system used on the Mk-48 following IMA overhaul is a set of 8 ft cabinets about 30 ft long.
Assembly of a warhead or major sections of a weapon together would invariably need to take place in a magazine or specially designed space, not something you're going to do just randomly on the hanger deck. Think of it like major work on a car engine - you're not going to want to do so outside of a clean enclosed shop with the right tools available.
Truly a sad day.