Ever since Windows Update v6 has gone live, I've seen a lot of systems that had Windows Updates turned off due to one simple fact. I complained about it during the beta but it was too late in the process to get it changed and I don't think it really was on the radar of the developers anyway. The annoying 'Updating your computer is almost complete. You must restart your computer for the updates to take effect." reminder that pops up constantly until you reboot. True, you can set the delay timer in the GPO but the upper bound on the setting is too low for my tastes.
I agree it is important for people to reboot to get the updates fully installed, but if it comes down to people disabling it due to how annoying it is, I think there should be a toggle for it. Today, I patched a Windows XP SP1 machine due to this problem. It had 76 updates waiting for it, including SP2.
You can short circuit the reminder by turning off the Automatic Updates service after you apply updates, but that is a bit of a hassle. A lot of times you have to wait until afterhours to reboot a machine you just updated.