Suddenly all of my iCloud Notes are being dumped into one "All iCloud" folder on my iPad and iPhone, but the subfolders which used to be there are no longer visible. On my Mac, all is as before with my hundreds of notes located in various folders.
When looking at a note on my iPad/iPhone, I can see the folder it should be in listed under the note name and create date. Also, if I hit the EDIT button under folders, I can see all the missing folders listed.
This is a recent change, maybe related to the new Mac OS (Catalina)? I'm still running Mojave on my Mac, but all the IOS devices have the latest (13.1.2) software installed. It's a true PIA to try to find a particular note by scanning through more than a 1,000 of them.