A pinhole exposed to a vacuum isn't a terrifyingly dangerous thing. You could probably stop it with your finger, and you might not even get a blood blister. You're sharply limited by both the the speed at which air can travel in to the vanishing region and the volume of air that can be extracted in any given moment. The area of the skin involved is stringly related to what happens next. You won't get hit by flying debris if you don't leave the power on too long, and if you slowly shrink the area of affect down you won't get smashed by the air entering the vacuum region around you, either.

...but that said, your other observations about the effects seem entirely reasonable.

@StarfishPrime, :-) For the record, the smallest example I used was a dime. I'm not convinced Hollywood is right all the time, but if it's to be believed (hah!) that's enough to suck a nearly indestructible alien through. I'm not sure what a pinhole-sized or even a dime-sized event would do for our superhero (probably a whole lot of nothin'), but I'm willing to stand by my generalization: Bad Things Happen (I wonder what his nearby skin would feel like with a pinhole-sized event? Would the hair yank out? Ow!)

Are you sure it was the thunder, and not the voltage differential between your feet?

@Harper, :-) That's a great question, especially since that bolt fried electrical lines and phone lines in the walls of my house. However, yes, I'm sure it was the thunder - which, at the distance I was at, is better described as a "compression wave" or a "blast front." Electrically, a quarter-mile is a long, long way to actually discharge electricity through me to ground. My rubber-soled sneakers would have been a problem, and the result would have contracted most of my muscles, which didn't happen.

@JBH have a look at the case of Jerome Apt on STS-37 for an example of a 1/8th inch hole in a spacesuit being sealed by human flesh with a small scar as the long term consequence. Guy didn't even notice. Whatever the minimum hole size for Bad Things is, it'll be at least a little larger than that.

Oh, a reread of the OP brings up the critical detail, "It also doesn't affect living things". Basically, the hero will eventually be killed by a bird or nearby pot plant once the wind gets strong enough. Or an angry, naked supervillain.

@StarfishPrime, I don't doubt your assessment, I just didn't use a pinhole as my example. Are you confusing the molecule-thick vacuum zone with a pinhole event? Your observation has more votes than my answer, and it doesn't even address an issue with my answer.

@JBH just adding a reference, for the benefit of those not already familiar with the story.

I find it difficult to believe that a lightning strike a quarter of a mile away, blew you off your feet! If that were the case, many things would be regularly knocked down by lightning - yet there are no reports of this. For the record, I've been about 100 yards from a lightning strike, and while I "hit the deck" voluntarily, I was not blown off my feet. One final anecdote, my brother was about 15ft from a lightning strike that hit a CB base station antenna, and claims he was literally knocked out of bed.

@JBH Could you explain your third footnote in more detail? What makes you think that it would punch a hole in their hand? When they ended the effect, a dime-sized area (2.5 cm^2) times 2 cm means 5 cm^3 of air would rush toward their hand at, let's say, 500 m/s, the mean speed of air. That's a momentum of just 3 g m/s. For reference, a paintball is about 3 g, it moves way faster than a meter per second, and it won't put a hole in someone's hand. I feel like it's easy to get carried away looking at just the wind speeds without thinking through how much air is really moving.

It was a bit of hyperbole, but let's look at the facts. A tornado "can drive straw and blades of grass into tree and telephone poles." And that's just the wind force of a tornado. The tornado wind speed record is 441 fps which is high-end Airsoft speeds (remember, blade of grass into telephone poles). If your SH "activates" a dime-sized space over the back of his hand and allows the wind speed to build up, the force of that wind against his hand when deactivated would shatter bones and possibly puncture the skin.(continued)

But that assumes that only wind is involved. If a piece of concrete or metal is moving at that speed (even blunt) you have a very good chance of driving it through his hand (in fact, it most likely will). Now, we have tornado+ force winds whipping around your SH who's standing literally at "arm's length" to the source of those winds. Winds that can move train cars off their tracks. It's going to throw him all over the place, and if it happens to bring his hand into contact with himself.... Yes, you said that everything inside the perimeter was protected, but there's some fun stuff here.

@GlenYates, I don't know what to tell you. Lightning, fell down, wind knocked out of me, house wiring burned out. Maybe it was closer, but your disbelief means absolutely nothing to me.

The lightning channel is not a pure, unadulterated electron flow, it is extremely hot, conductive plasma. It is hot, therefore it expands, which is what causes thunder, not the air rushing to fill it back in. That makes the rest of the conclusions irrelevant.

@JBH I suspect, given what Glen says, that you fell because your loss of consciousness rather than the sheer force of air.

@JanHudec unfortunately found a fatal flaw in that answer. Also, I wonder how much of the knocking-down effect was due to the eddy currents from the massive magnetic field generated by a lightning strike. It has been known to electrocute cows at those distances on occasion, by creating electric arcs between their legs.

I think we should ignore the lightning part of the argument - my understanding was that it was just to show that individual atoms vanishing do not produce sound (which, yeah, I kinda figured the wind would be more important, setting aside the point that it doesn't really make sense to talk about sound at the scale of air molecules anyway).

@JanHudec "As the superheated air cools it produces a resonating tube of partial vacuum surrounding the lightning's path. The nearby air rapidly expands and contracts. This causes the column to vibrate like a tubular drum head and produces a tremendous crack. As the vibrations gradually die out, the sound echoes and reverberates, generating the rumbling we call thunder.." I've never heard anyone claim the expansion of the plasma alone caused thunder. Can you cite anything?

@Eth in what way what Jan's statement a fatal flaw? Most of my answer is a frame challenge that suggests wind speed would have substantial side effects - which has nothing to do with how sound is created. I've asked Jan to cite something to prove his/her beliefs. A quick google search doesn't support his/her beliefs.