You could put all the fuel in the nacelles, say - but they are already very, very small for their supposed performance of warp nine'ish (heck, the whole scout is, almost shaking my belief in size being a prerequisite for speed in Star Trek).
But much of the rest could be in plain sight. Only on a large starship would one bother with "Jeffries tubes" and vanity covers; on an Archer
, life support systems and the like would be lining the walls and ceilings, and be constantly accessed by the crew because of the lack of redundancies and the subsequent greater need of maintenance. "Rooms" as such would be of limited use, unless they were filled with useful things like tanks, valves, stem bolt manifolds and the occasional bunk in between.