This issue is solved by the new Metanota v2.1 by using the "new" Simplenote API.
It's nothing I can do in Metanota to prevent that and deleting and reinstalling it would not help, as the "zombie" folders will be sent back by Simplenote over and over again.
- open your browser, go to SimpleNote's webapp site and login as usual
- from the Web interface export your notes to a local CSV/XML file, delete your account, create it back and import your notes form the backup. I've did that recently and all the zombie folders problems were gone (for a while)