Submarines that had stern tubes did not always have a second hatch. It's easy to identify torpedo hatches on a plan because they are angled. There were round hatches in the deck, usually angled at about 45 degrees, through which torpedoes were loaded into the sub. Loading torpedoes into a U-boat was done by the same process used on any other submarine. That part of the sub is out of the water when it's surfaced, of course, so the crew would remove the deck panels above the torpedoes and load the torpedoes into the torpedo rooms inside the pressure hull using essentially the same procedure they would use in port. U-boats that had externally stowed torpedoes simply had them stored under the deck, but outside the pressure hull. The flat deck of a U-boat is part of the outside hull, as is much of the sail/conning tower.
You're probably aware that submarines have an inner pressure hull, which is strong and cylindrical and meant to keep out water, and an outer hull which is meant to give the boat its hydrodynamic shape.
