There are various security exploits a user can use by creating hidden files on an ftp server
Just for example ( and i haven't left my network open to this, i am just being cautious ):
a user can create a .ssh directory and put in it the keys they require to connect
a .forward file, to forward their mail through another program and possibly be able to change their shell. ( assuming I had sendmail running )
While I have minimum services on the server running and I am not aware of any such vulnerabilities on my server, I still go by the motto " you can never be to cautious when it comes to security" and given that most of these exploits utilise configuration files that are usually hidden, and I am required to give them write access to their home directories, I figured If i stopped them from making hidden files it would add a bit of extra security to the system.
If it can't be done though, doesnt matter.