Should I pause mirroring when I reboot the witness server?
You must do this in order if you want to update the Principal, Mirror and Witness:


Switch from high-performance mode to high safety mode (if you are using this mode)
Remove the Witness
Upgrade the Witness (anytime between 2 and 9, see below)
Upgrade the Mirror(s)
Wait until Mirror(s) is(are) synchronized and manually fail Primary over 
Upgrade the Primary
Upgrade the Witness (if not already done between 2 and 9)
Switch back to high-performance mode (if required)
Add the Witness