Surely it's been mentioned before but the vertical shaft from TMP was envisioned as a power transfer conduit from the reactor to the impulse engines as well as the warp nacelles; the reactor itself was far below decks at the very bottom of the hull. Thus it is "vertical" only because the impulse engines are fairly far away from the reactor. Reliant's vertical segment would be only high enough to connect the reactor to the engine, so the guy who fell over the railing wouldn't have fallen far
The TNG warp core simply works differently. No particular reason for it to be vertical except it used the same set as TMP and they needed to fill that space with something meaningful.