I don't see any reason why you couldn't create a multi story ship the same way you create a multi story building. You could have stairways and or ladders and if you really wanted to jaz it up you could even give it some addactions (available only on the bridge ?) that allowed you to set velocity or change direction.
In fact, I was JUST about to do the same thing myself ! Not the modelling part, but taking a stock standard tank transporter and giving it "Port 10", "Starboard 10", "Flank", Cruise" and "Dead Slow" addactions.
Mr P - this might not help you (addaction aren't v1.0 compatible) but if you want I'll see what I can do with a ship in fixed motion.
roni