And the munitions are supposed to depart from the aircraft how, exactly?
Currently, bombs are kicked off downward and sometimes a little bit sideways as well. There is a small shotgun size charge that pushes an ejector foot down, that propels the bomb away from the aircraft. This, of course, works in conjunction with gravity.
A bomb bay on top would have to have a LOT larger impetus to get the bomb to clear the aircraft.
Missiles are a different thing. They are self propelled, going forward. But still need some clearance from the aircraft body.
Fuselage mounted missiles such as an AIM-7 on the F-15 still need to be pushed away from the body before firing the missile motor.
There has been at least one aircraft with over-wing mounted missiles, the Jaguar GR3.
The weapons bay doors are only open for a short time.
Even as far back as the F-106, you could go from completely closed, open, launch all 4 missiles, close bay doors in about 4 seconds.
And from a personal experience aspect, loading bombs into a top opening bay would be a LOT harder.