As you found flaminus, check your guns crew before you do any "upgrades". This is the idea of the Green circles at a lot of the home ports - to be a reminder to the player to Save prior to entering port, which is near the smaller red circles. Also remove the crews from the guns, and put them back where you found them. Then you can safely enter port and dock, and ~most~ upgrades can't harm your people... maybe.
As you experienced on a new start and changing deck guns yourself, you have to Save the game so that the game engine properly initializes your gun crew positions at the new station(s). Usually, what you will find (if you don't Save) is that the location where the original gun was will be where the gun crew will properly report to their duty stations, while the other gun crew is in the torpedo room, sipping the juice...
As for the number of gun crew positions, remember first of all, it is now a deck gun, and as such, it must be fully manned as per union agreement. A deck gun is a deck gun, after all...
- I jest, but only on the union rules. The game dictates that what we do to the one deck gun, must be done to the other also (crew-wise), else we can't swap ends with the guns... Maybe if we had "auto" stations, the way the Stock game does things, we wouldn't have the issue, but FotRSU, in a early attempt to eliminate the gun problem put designated crew member in the gun slots, so it is what it is. It does eliminate most instances of missing gun crew positions.
Also, the game does not allow us to man that 2nd deck gun, whether it would be a 4" and a 20mm, or a 5" and a 20mm, or two 5" guns. There is only one position the player can jump into, and that is the "default" deck gun position for the boat, which on a Gato is the bow position. The 20mm deck gun will not shoot at airplanes, only surface targets... sigh. So don't expect some help for your AA crews on the conn positions. But definitely check your gun crew positions both before and after any changes you make to the guns.
btw: I was able to completely hose the gun crews on both the deck guns and the AA guns, just by trying to experiment a bit with the Gato... I don't like the idea of one little mistake trashing the boat like that... I'll do some tweaking on the in-progress careers, to see if similar can happen there...