If that user has a website, as evidenced by a "mydomain.com" type folder, then no, you shouldn't delete those folders. Maildir holds your mail, and Logs is for the webserver. You don't own them, so you don't have permission to delete them.
When you first set up a user, you do get an empty directory. It's when you create a domain that's owned by that user that the "logs" directory shows up. Nowadays, there's no more Maildir (AFAIK) for new accounts, since all new account mail is stored elsewhere.