Once again, it is not an imaginary issue but just not unsolvable.
LM has done a lot of tests during the DT&E phase, 70 launching have been carried out with 4002, 4003, 4005 and 4007. Engineers have built up database on static pressure, dynamic pressure, sound pressure, ammunition AoA, ammunition location and geometry...etc while the bay door is opened.
For example, when F-22A opens it's main weapon bay in transonic phase, the shockwave located in the front and at the end of the bay creates 170dB of sound pressure (equivalent to the sound pressure mesured at 1m away from a F-15 flying with full afterburner), and this induces a 50-60Hz vibration to the structure, which is closed to the resonance frequence of the aircraft structure, which may damage the structure.
USAF has spent more than 5 years to integrate AIM-120 to F-22's internal weapon bay, more than 100 launch tests done, before being able to establish the correct launch envelope.
I've read in a technical article than RCS or IR signature is not the main issue of internal weapon bay, but all physical impacts on the aircraft and also to the missile itself during the opening of the door are critical.
Henri K.