Ctrl Alt Del,
I think I saw the reference to the 18 brachos of Shemoneh Esrei corresponding to the 18 bones in the spine brought in the Gemara (4th perek of Brachos), which would not make it some middle ages mystical thought to have. As I recall, the reference to the spine was brought in a discussion of how to bow during Shemoneh Esrei (if physically capable, one should bow deeply enough so that the bones of the spine in your back protruded).
Now, I doubt that the Tanaaim were unfamiliar with the human spine. How they were counting was likely different than how we count today (perhaps they didn’t count the portion of the spine in the neck as part of the 18, for example, since we were talking about the position of the back when bowing). I’m not an expert on anatomy.