Of course they'll work. If fighters and spaceships can fly around with people inside, shuttles can, too. You may not be able to walk around inside them while they fly, but they'll work.
And yes, if they're in, I say give them all the guns they have 'in reality'. The tail gun and the forward-firing ones. Bring it on
.
"One of the bitches actually gave birth while she was attacking, and her puppies joined in on the carnage."
--the awesomeness that is Boatmurdered.