Hello,
If you turn Desktop & Documents off for iCloud Drive settings do they show back up?
Use iCloud Drive to store documents on your Mac, iPhone, and iPad - Apple Support
That feature doesn’t create a second Desktop Folder it moves your existing Desktop Folder to iCloud. If the missing folders are treated like excess storage they may be in your Home Folder still. That is likely a better place to save the folders if you still want iCloud Desktop & Documents but don’t want these folders in iCloud.
”If you can’t move or save a document to iCloud Drive, your iCloud storage space may be full. The document stays on your Mac, and is uploaded to iCloud Drive when space becomes available.”
Folders that come with your Mac - Apple Support
Go directly to a specific folder on Mac - Apple Support
I hope this helps.