I prefer the aft deck gun, in TMO's optional mods, I always pick the "aft gun only" mod. It's by no means a handicap. When finishing off a wounded ship, all it takes to bring the gun to bare is to maneuver before you surface.
Richard O'kane preferred the aft deck gun for the fact that the only time he would need it was while heading away from trouble. Historically there was more deck room for the gun crew to operate on the aft deck. It's possible that it cut down underwater drag for the boat as well.