Imagine swooping in to a inhabited planet with your weapons out feeling all badass, when suddenly you smack into the atmosphere and the hull rapidly heats up to about 3000 degrees, cooking off the ordinance in your deployed missile launchers (which you can't really unload in space.) Not only did your ship just crack up from the detonation inside your shields, and you just got vaporized immediately, but you also just sent a 48 ton fusion reactor freefalling on an unsuspecting populace which will no doubt cause some consternation when it hits the ground. I think its rather important to be able to retract your weapons inside your hull. After all, we must comply with all year 3301 OSHA safety standards.