Well, for Colossus, I believe that the superstructure and engines take a helluva lot place, perhaps over 50% if you ask me. Still, I guess that the crew would have quite some luxurious quarters, at least compared to those on, say, an Orion.
Also, the ships have to be big. Lets not forget that a FS- era Interceptor missile has a payload of 18,5 Kt. 18,5 Kilotons. The Fat Man bomb dropped on Hiroshima had 21 Kt. Now, a Harbringer has 5000 Mt payload - whereas Tzar bomba, the single most powerful bomb on the Earth, had 50 Mt. Do I have to say more ?
My 0,02$.