Main ammo and fuel storage, sure. But you can't avoid having fuel and ammo present in the pods, not if you want to refuel and rearm your birds anyway. I suspect they'd have smaller storages for both, in which fuel and ammo is transferred as required.
Master_Drow - about the struts that keep the pods in place.. those things are huge and bulky. It would take great amounts of time and firepower to "saw" through all of them to separate the pods from the ship - and I doubt a battlestar and her viper complement would just sit still and let you do that to it
And with the amount of precisely directed firepower you'd need to spend on doing that, you might have just as well directed it to a more critical area of the ship, something that would cripple or destroy it for good, like punch through to the main tylium fuel lines/tanks, take out the main reactor, or something along those lines.