This is not true - on every rehat system since 8.0 I've been doing this. No machine had reduced funtionality because of it. In fact, the opposite happened. Try for yourselves, then tell me.
[bevan wallace ~]> sudo reboot X11 connection rejected because of wrong authentication.
[bevan wallace ~]> sudo /sbin/reboot Broadcast message from root (pts/0) (Wed Jan 14 17:36:35 2004): The system is going down for reboot NOW!