damkiller I did a test and the crew actually was clever enough to stop standing in the empty ammo factories and went to recharge the shields. Might be I was lucky, just saying I didn't need the bunks during my tests.
Also changed some structure, replaced the normal cannons with lasers to solve the ammo issue and removed the third crew quarters in your 'diagonal' thruster modules. Oh, you forgot to give the center and the outer thruster modules some FE btw.