Unusual Shortcut, Menu Override in Evernote
I can replicate this if I set the Paste Without Formatting Menu item to have an hotkey using the system Preferences 'keyboard shortcuts'.





I set the shortcut in 'Application Shortcuts' and the chose Evernote.app rather than All Applications.

Removing the Setting will put things back to normal.

Update:

Since the OP. Confirms they once did set a global hotkey and since removed it. But the menu shortcut persist. 

I re-did my global hotkey and  then deleted the reference from the com.apple.universalaccess.plist file.  

This resulted in the global hotkey being removed from the System preferences global shortcuts. But in Evernote the global shortcuts still appeared.

This is what the OP. seem to have.

My simple fix for this was.

Re do the global shortcuts for "Paste Without Formatting" in the System preferences global hotkeys. Giving it a new shortcut.
Check to see if Evernote picked it up, which it did.

And then deleting it in the System preferences.

This removed it from Evernote.