Probably edit the /etc/pve/storage.cfg
file, removing (completely) the relevant storage entry. Reboot the node & you are probably good. After that you probably will be able to delete those no-longer needed directories. (Be careful what you delete!).
If the relevant storage you wish to delete is mounted storage you may have to edit the /etc/fstab
removing that entry to stop it remounting on reboot.
NOTE: HAVE NEVER TESTED THIS.