I am currently using the scrivener-bookends-Word-combination for articles, but for the final manuscript of my dissertation, I am considering switching to LaTex. Is it possible to scan TEX documents or maybe the scrivener document itself?
You can scan LaTeX docs (I think!) if you tell Bookends to use BibTeX citation delimiters. I haven't tried this much, myself, because I don't use LaTeX.
As for scanning Scriviner docs, if they can be saved as RTF (and I'm pretty sure they can) then you can scan those.