I also do not think this was ever an intention of the HUNH. It is unlikely that any coach could have foreseen, much less banked on, the idea that faster play would mean officials missing calls. IMHO, this whole mess is a result of officials not taking control and ensuring that the integrity of the game come first. I think they felt/feel pressure to keep up with the offensive player and they feel the pressure from coaches screaming for them to hurry up and set the ball. I also doubt very highly that any coach or team, Auburn included, would switch to this offense based on the idea that they'll get a few extra no calls per game.
Rather, I think that the HUNH just breaks the whole system down. It creates a bit of chaos and I think that players and refs both fall into it. Defensive players are suddenly exhausted, refs are missing calls, and offensive lineman are often down field way too early. This all sounds to me like mental fatigue, not physical. Not saying that the HUNH doesn't cause physical fatigue....obviously it does. But IMHO it's the mental fatigue that causes most of the problems for defenses and refs.