I'll note that it was written before the model redesign. Stealth bombers are significantly larger than their former T1 models, and the fluff about how tight it is in there would make more sense for the old models than it would for the new.
Torpedo launcher are huge (and sunk into the hull), cargo (ammo) space is likely a big part of the ship, too.
:Edit
Re: Crew
It's a bit difficult, because the majority of ship uses are not extended ( no stop at a station for a few hours ) by any means, so it seems to be a bit excessive to put a couple of hundred guys and gals on a ship into stasis pods just 'because'. In the same line it would be remarkably cheap to say "See, I fitted this ship for combat and just veered out on a 2 minute cruise - of course it was empty!". PF states that there's a minimum amount of crew for basic duty, which means flying an 'empty ship from a to b', or whatever the quote on the panel was. It's also stated that the crew only does minor maintenance works. But it's still safe to assume that you don't need 500 janitors on a battlecruiser at all times. When I envision the work done by the crew 'Damage Control' is what comes to mind. The majority will be done automatically - decisions fused by the capsuleers commands and automatic expert systems - but when things explode it is safe to assume that there'll be a lot of confusion and minor damages throughout the whole ship, which is a pretty complex piece of machinery, which is usually code for "Does not react well to being shot at". Depending on how we envision damage penetrating the shields and especially the armor to happen there might be quite some manual work to be done to keep things in control. Security is also not a dirty work.
But yes, generally speaking, there's a lot of incoherence regarding the actual jobs of those hordes of people on those ships, especially since 100% of what the crew does/would have to do is not covered by or hinted at by the game mechanics, which additionally have the ship work in a way that makes it possible for one person with two hands to operate it perfectly all the time until it explodes in a true on/off fashion.
Regarding Graelyn's warp speed thing: I would gently discard some of the aspects from the novel, because at least those incidents in TEA were talking about a) a shuttle with civilian passengers and b) an old ship. But even then, I would reduce it to the need of 'reinforced' areas in the ship that the crew'd have to get to. I'm less thinking of those stasis/escape pods but more specifically shielded / stabilized areas that make warp transfer bearable for those working there, ideally coinciding with the location of escape pods.