This is a recurring issue for me. When I delete a folder with many files and subfolders in my Cryptomator vault, the deletion will often not be complete. For instance, if the deleted folder is named X and it has subfolders A, B, C, then X and (sometimes) A, B, C will remain showing as folders after the deletion, even though most files have been deleted. When this happens I have to execute a delete command on X a second, and sometimes even a third, time before the folder is fully deleted.
This is on Windows 10 with a WinFSP drive. I usually delete by right clicking the folder and selecting delete from the context menu, or by highlighting the folder and pressing the delete key on the keyboard.
I have noticed the same since at least the much older version 1.6.17 which I still use on a particular PC. If I remember correctly in some cases I had to delete the inner empty folder before the outer ones could be deleted. Initially I thought it has to do something with dropbox syncing during large number of deletions but I might be wrong.
I have the same issue with you using Cryptomator mounted vaults. Also I use rclone encrypted mounts and get the same problem that the directories don’t purge fully.
This may not be a Cryptomator issue but a Windows File Explorer or an WinFSP issue.