Yep just set the depth a little lower. The deck's going to submerge with the crew still on the tower. In reality this had two advantages:
1. The dive tanks are pre-flooded and the sub will dive faster.
2. The sub presents less of a silhouette for the enemy eyes and radar, since only the tower is above the surface.
In the game I didn't find the setting to have much of an effect on either of those two things, but it greatly adds to immersion when planning a night sneak attack
