Does anonymous FTP really need Maildir and logs folders? I'd delete them if they were listed in the panel interface, but they're not.
Also, I used the panel interface to try to delete the /incoming folder, but that didn't take, it's still there.
I will not suggest you to delete Maildir and logs directories. You will definitely need logs for debugging, troubleshooting, or maintenance stuff.
there's no real need to go around deleting things. Is your home directory too cluttered?
This isn't my home directory, it's very specifically for anonymous FTP file storage. Extraneous folders are distracting and inelegant.
Those folders are permanent. I suppose Support could delete them if they really wanted to, but I suspect it's against the rules for account consistency, or it'd break something.