It appears that the directory ownership on those directories is not set correctly which is why those folders cannot be deleted.
However, there should be no harm in keeping them. It won’t affect other websites and it won’t affect your ability to host the domains on the same or another account. The only downside is that they consume 2 inodes (out of 60,000) and that they don’t “look nice”.
But sending this up the chain to a server admin because it doesn’t look nice in the file manager is not really justified I think.