I tried TMO when it first came out, decided it was as much fun as listening to a class full of second graders trying to play Honky-Tonk Women on recorders.
So I went back to stock game with Webster's GFO mod, and DID have occasions where the deck gun slots vanished into the 5th dimension after changing from stern to bow with the stock game. After that I started every career by moving the gunners up into the damage control section, leaving the deck gun slots empty, then changed to a bow deck gun before moving the gunners back into the slots. Get a new sub repeat same procedure, making sure I had a bow deck gun before leaving the office. Doing it that way I never saw the problem again, but always always change to bow deck gun at the very start of a career like it was a holy ritual.
I never tried RSRDC or any mod with super crewmen, but I have read some posts here and there discussing the addition of extra crew slots and special abilities. The first thought that struck me was that unless that's done just right it could cause crew slot glitches in unexpected sections at random times. Dunno which mods have them and which don't, but that would be the first place I'd look for this recent flood of disappearing deck guns.