While I have used about 8 notebooks to organize my notes, with tags as well to further organize, I too have ran into the dilemma of having to think to much about what notebook to assign some notes to that could be in multiple notebooks.

One reason I would see to keep notebooks in a separate notebook would be to share notes with another Evernote user although my notes are mostly Home related and I’m the only Evernote user in the Home at this point.

A second reason that I would personally find more useful would be the fact that I can mark a notebook for offline access on my Android phone. I could see the value a separate notebook for a particular vacation, to keep those notes handy.