Oh certainly. Especially in the case of missile tubes, a lot of ships only carry enough rounds in the magazine for a single tactical engagement, and if you're enthusiastic enough with them, running dry is very ready. It makes sense that this only represents the 'ready' magazine, with many more missiles in storage. Big cargo bays also make sense for NAC-heavy ships. I forget where, but I recall fluff saying that the fusion charges used to fire those are VERY hard on the barrels, and that ships tended to carry spares that they swapped out during downtime.
(By the way, stuff like this is actually why the Soyal-class has mech cubicles: the initial idea was to carry LoaderMechs for pulling those gigantic Mass Driver shells out of cargo, and then that got expanded because the designers had poor impulse control and lived in a universe even more obsessed with mechs than us fans are.)
Another benefit of big cargo bays is fuel. WarShips *can* recharge their drives with conventional sails, but in an active situation it makes much more sense to skip that and just reactor-charge things while maneuvering and fighting in-system. That uses up a lot of fuel, especially if you're also charging an L-F battery at the same time.