Thanks @BSR for the update! I would also like to add for anyone else waiting for the fix, that I just upgraded to Yosemite 10.10.5 and the Evernote icons are now visible again! So if you are in the same situation with 10.10.2 or an earlier release, an OS X update might help you return to normal icon visibility.
Same issue here (OS X Yosemite 10.10.2, Evernote 6.11). Without the icon visibility, Evernote's been quite difficult to use for the past three weeks. Any news on an update? Or as previously asked, can we revert to a previous version until a fix for 6.11 is available?