Why do I still see my manually-deleted photos in Photos in OS X El Capitan
I was facing the same problem.  Not only were the pictures still being displayed within the Photos app, the pictures (and their folders) that I have deleted manually in the Masters folder, have reappeared in that folder again after when I clicked on a few images within the Photos app.  The best way apparently to permanently delete the pictures would be to do so within the Photos app (see http://www.imore.com/how-delete-images-and-videos-photos-os-x#delete-permanent).