Federation and Klingon ships at least don't carve big holes through the center of their ships.
But they do! That's the thing you easily miss if you don't think it through... An empty, wasteful space is an empty, wasteful space even when it isn't surrounded by structures from all directions.
There is a whopping big empty space between the nacelles of every one of the Enterprises
, just like there is one between the nacelles of the Romulan ship. But the Feds don't even put a ski-box on top of that space, so they use the volume much less efficiently than the Romulans.
There are select few Federation ships that don't carve this giant cavity in between the nacelles; the Nebula
class is one of the very few major designs not to have this feature. But funnily enough, every Romulan design other
than the D'deridex
places hull elements directly between the nacelles: the old Bird of Prey (or whatever), the scoutcraft, the science vessel and even Senator Vreenak's yacht all have the nacelles flanking the hull, rather than a cavity.
Also, given that the only parts of the waarbird that we ever saw with windows are the beak and the horseshoe at the back, it looks like only a fairly small part of the warbird is actually habitable.
By that token, Kirk's TOS ship did not have any crew facilities in the saucer section...