well what mods are you using?
GWX from the sound of it.
if so, this has been addressed by modders. if memory serves me, in the stock version of SH3 any AI u-boats had no watch crew visible and no armament other than the aa gun (ie no deck gun at all)
because the u-boat deck gun is specific to the player sub it couldnt only be a work around of putting the small 5" gun in its place for AI boats.
someone else who knows more might better explain, but i believe that this is correct. so in essence, modders are the reason the AI boats even appear in the campaign and have ANY kind of gun on them at all
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