Since you can’t delete subdirectories, you could at least have the option to hide them so you don’t make the files a mess.
Sorry, but that’s not an option. If they’re really annoying you, you can remove the domains you use from cPanel and take a backup of your site and create a new hosting account with that domain.
You can rename them to start with a dot. That’s the way to do hidden files and folders in Linux.
But most FTP clients don’t actually hide “hidden” folders, so for all intents and purposes, there is no way to hide folders.