I see you unchecked the folder, but my question is, if you are 100% sure the content you see comes from the unchecked folders. Because this is the issue (as far as I understand you) that you can see a content of unchecked folder, right?
To be honest, I don’t know, how to remove the content from already unchecked folders. So I would try to enable it and then disable (uncheck) again. Cubase will ask you, if: Remove from Database folder name. Click to Remove, please.
You should also be able to find the (hidden) mediabaydatabase file in the folder (in File Explorer or Finder). If you delete it, the folder should become invisible for MediaBay.