This hasn't really been an issue yet, users don't usually remove the .dotfiles anyways. Theres really no easy way to hide them, as linux dont allow you to hide system files.
Use or for that matter Abuse, depends on user's tinkering.
You may do it too, but after creating full backup.
You may learn a lot from these sort of things.
*I guess that bloke also learnt a one,if didn't backed up.
Nothing to do with the .htaccess file
And even if you block it from the ftp daemon, someone will just use webdav/cpanel file manager/a custom written cgi to do it for them.