MTM, GrumpyMonkey, good call re: direct download. It's working now. What a pain in the ass, but it's working for me now so whatever. For future comers: give up on Apple Store version, and try the direct download: http://evernote.com/download/get.php?file=EvernoteMac
I see the exact same structure as romiem (post #122), and I also can't see any results on spotlight, including newly created notes. I actually deleted the whole subtree after com.evernote.Evernote, and rebuilt my collection with sync, and still no joy. I'm on Version 6.0.13 (451658 App Store) of Evernote running on OS X Yosemite 10.10.3.