Interesting...do you mean there's a door behind the rear gunner's station on the upper fuselage?
The only thing i can think off for having one would be to rotate the gun blister so that the gun lies near to the fuselage, open the door and slide the gun into the compartment to reduce drag (something like the "retracting" guns on the SM.79). Far fetched i know, but i couldn't resist taking a wild guess
Edit: Since you mention the blister is to provide clearance for the bomb racks, i came up with another idea. Supposing the bombs are not armed during the start of the mission, then a crew member would have to arm them in flight like in the "memphis belle" movie, where they take the locking pins off the bombs in the B-17 bomb bay. Since the Ju-88 is a lot smaller and maybe doesn't have enough internal fuselage space for a crewman to get around on a standing or semi-upright position, could it be that they opened the top of the fuselage so that he could go into the bomb bay and arm the bombs?