I really appreciate the fact that you seem to be thinking this through. Your inter-deck stuff is similar to what I've been doing. I have a ~.65m inter-deck space, typically (see my WIP thread if you want to know the specifics).
However, I do have a few locations in the ship with sub-standard deck heights (basically at the primary and at the secondary hulls in the general vincinity of the interface), and I will have "crawlspaces" in those areas. I'm only going to call the engine-area crawlspaces "jeffries tubes" however.
A side note... if you look at the refit 1701, there's an entire ring of sub-deck-height space on the underside of the primary hull. This isn't a "jeffries tube" either... but it is a technical space. I always found it odd that TNG-and-later-era Trek showed the massive tunnels going through the entire ship. This never really made much sense to me... why not just have the stuff right there in corridors (behind access panels, or under floor panels, or whatever?). With a <1m inter-deck space, this would be easy enough.
Anyone have thoughts on why (other than to reuse a claustraphobic setpiece) they had these funky little crawlspaces everyplace? Has anyone ever tried to lay out the "jeffries tube" network inside of the Enterprise-D or the Voyager? I doubt that there'd really even be space for them... but it did make for some interesting technobabblish storylines!