That is most likely the same-ole same-ole on the deck gun issue, but since the submarine has one assigned with no choice for the other position, it was hoped that all upgrades would go there. Apparently not so. On what kind of screen were you offered the upgrade to the 4" gun? Just the regular Captain's Office between patrols, or did you get a separate screen stating that you qualified for a new gun? Either way, we may have to make the gun positions for the specific submarines more prominent for the player... The question is still there though, as to which gun is which? When you go to the equipment screen and click on the guns, is the rear gun still a 3", and the fore gun is your upgraded 4" gun? Also, we might have you back-up your Save folder and have you do the old "fix" for the crewless gun, and see if you can get a crew on it... if you want to try that. ??
btw, as a little side note: Some of the Sargo boats and fore and aft deck guns, like the Narwhal did... so you are not "un-historical" here...