Need to Know

The first nugget of information required here is the source of the popup reminder:  the service appropriately named 'Automatic Updates'.

If you just want to stop the reminders temporarily, pop open a command prompt (may need elevated authority in Vista/7) and enter:

net stop "Automatic Updates"

But that has a fairly big disadvantage:  You will not receive any more updates until you reboot your PC or restart the service.

The Solution

If you are set to look for Updates at a specific time each night, then you will want to make sure the service is running before that time.  To ensure this happens, modify the above command using 'start' in place of 'stop' and drop it in a batch file.  Then open up the Windows Task Scheduler and add a new entry to call that batch file about an hour before your scheduled update.  This should prevent you from missing anything critical.

To take things a step further, you can completely silence the restart reminder during your workday by scheduling the service to stop before your normal workday begins.  I would not recommend this if you do not regularly reboot your computer though, because you will never see an indication that a reboot is required.  Whether or not you feel comfortable taking this option is up to you to decide.