I've had this issue for a long while, but I just installed El Capitan and thought that might take care of it. Although it indexed everything else for the new Spotlight, Evernote notes were nowhere to be found. I followed instructions upthread and deleted my App Store version, restarted, downloaded the direct version. When I logged in to Evernote it copied all my notes in and said it was migrating. I checked Spotlight and saw that it was re-indexing. It took several hours - I have a lot of notes. Then when it was done I searched for several things but no Evernote notes showed up, not even in Finder. I tried to force a re-index using the terminal method and some others but no dice. I looked at the CoreData file and it was dated just now, so it's obviously up-to-date, but Spotlight isn't seeing it. I deleted the file, quit Evernote, and restarted, but still nothing. I checked CoreData and it recreated the directory and files. I created a new note and searched for that, nothing.