The Crush and Sculpt algos have a basic noise gate built in, but I cannot find anyway to turn the gate on/off in the pedal itself. Can this be done or can it only be changed and then saved within the H9 Control software?

The noise gate button is where the tempo mode button is, and I think you can turn it off and on on the H9 itself in the same way that you turn tempo mode off and on — you press the left footswitch and the preset switch simultaneously (or maybe it's the right footswitch?).