In the new UI, (regardless of HwS vs Hopper 3) it was changed so that the box will not try to do the nightly update unless it was in already in standby. The only time you should see a message is when your TV is on and you haven't touched the remote for X hours after the end of the first program you watched, where X is what the inactivity standby is set to.
In order for the Hopper to perform the nightly update, all of the Joeys have to be in standby as well.
That being said, if a box hasn't done a nightly update for 72 hours, when it reaches that time, it will just reset with no onscreen messaging. Nothing will prevent this reset, not even timers.
As long as you leave inactivity standby enabled on all of the receivers in the home, there shouldn't be any issues. The Joeys will perform the reset anytime they are in standby overnight, as will the Hopper once everything is resetting or in standby.