Well, this seems to be a direct consequence from upstream behavior. Notebook has an optional delete_to_trash flag that will keep all files deleted in a hidden Trash folder. If this is not set, our case, it disallows deletion of non-empty directories.

Using the trash feature seems like a bad decision to me, we have a shared storage backend and files meant to be deleted should be deleted. As such, I'm declining this task, users may empty the directory before deleting them or use the terminal to delete with a single command.