Calibre goes to great pains to prevent foot shooting.
This happened after users did a really some really poor practice, like store the Library on the Desktop, and later cleaned the desktop

,. They howled that it was Calibres fault.
If you delete a (alternate) Library from the Create/Switch menu, you now have to use the OS to remove the folder and books..
The list of user induced problems is endless. Removing Empty books, that many use, other than by the Library view will not happen.