Hiding home shares on file sharing computer
If you set up their accounts in the Accounts pref pane on the server as "sharing only" then they will only get access to shared folders set up in the Sharing pane of System Preferences.

See the Apple docs on creating a sharing only account.

Since you say the email backup software requires that the user has real folders, then you can't remove them as "shares", they have full access to these folders and the server will advertise that.

Without knowing why the email software requires the user to have folders then a workaround is difficult to find.