Re: Vertical Warp Core?
I think it's purely a design standpoint for most Starfleet vessels. Federation starships tend to have their engine rooms positioned between an upper matter fuel tank (which may take the bulk of one or two entire decks) and a lower antimatter fuel pod area. What we see in most engine rooms is merely the end of the transfer shafts from each fuel source converging upon the dilithium reaction chamber.
"Shout, shout, let it all out..."