I agree its annoying, but i don't agree that bathtub around the AA gun is a bug.
Bug or not, i "fixed" it in my mod pack. Pretty easy to get rid of, just assign the boat the next conning tower earlier then youd normally see it. (next conning tower removes taht bathtub, and on the gato's cuts the shroud around the periscope shears. On the Tambor and gar it only removes the bathtub- thats how i know its not a bug
)