I read the following in the TMO manual today. Granted you are not running TMO but this may shed some light on your deck gun question.
Due to a hardcoded bug in the SH4 game engine, it is not possible to switch locations of the deck gun once a game has been saved to file. Trying to move the deck gun from fore to aft, or vice versa will result in the crew member slots disappearing. In order to circumvent this bug and prevent it to happening during play, the deck guns have been “fixed” to a location.