IMAP folder named Notes does not appear in Mail.app
With the advent of Mountain Lion, Mail.app has removed its Notes capabilities in preference of the Notes.app. This Notes folder is used (if enabled) only in Notes.app on Mountain Lion and iOS 5+.

What you can do is rename it something other then "Notes". You can change it to something like "Notes1" or "My Notes", and it will then appear as a normal folder in Mail.app (as an example).