Even though an email has been deleted from the user's email queue it moves into the trash area, so still uses disk space. To delete a email permanently and free disk space it needs to be deleted from the trash area (empty trash).

To empty Trash from Roundcube web mail in CPanel, follow the steps below:-

Empty Trash
1)Login to your Roundcube webmail
2)Once you are in Roundcube webmail, click on Trash folder at your left navigation to make sure your Trash folder is being highlighted.
3)Click on the “Option *” Button at the bottom of the navigation and select “Empty”
empty trash roundcube
Your Trash folder should be empty by now.