Often the server needs access to make backups, so when you get in and get root, you sometimes also have access to delete the backups.
It depends on how it's set up. If the server pushes the backups somewhere else and has write access, then the hacker can delete them. But if another account logs in to the server and makes a backup and downloads it, it's impossible for the hacker to access the backup.
Depends on if you planned for the scenario or not.