When a domain is deleted, SmarterMail deletes all files associated with that domain in the domains folder.  Once those files are deleted it will delete the domain folder as long as there is nothing remaining in it.  If there is something in there then it won't delete the domain folder as we don't want to delete something that an administrator may have put there for whatever reason.  In most cases the domain folder will get deleted when you delete a domain.  One other possibility is if there is some sort of lock on a file in the domain folder that prevented SmarterMail from deleting the folder - possibly a virus scanner, although we don't recommend running a virus scanner on the domain folders.