The actual diameter of a lightning channel is one-to two inches.1 (Source)
I had the privilege of being outside, walking for exercise in Texas, when a lightening bolt struck within a quarter-mile of me and my house. I was literally blown off my feet by the resulting thunder, which hit so fast my eyes barely had time to register the light of the lightning strike. Yup, it took me a bit to stand back up.2
So, 1-2 inches of channel diameter is enough to blow me off my feet. But before we start analyzing this useful piece of information, let's look at your situation.
The "channel diameter" caused by your superhero is zero. An infinitely thin surface that, whenever any atom or molecule touches it, said atom or molecule vanishes. How big is that channel?
No bigger than the largest molecule that touches it an any given moment.
How large a molecule is depends on the molecule, but they tend to be measured in angstroms or 10-10. I know that, worst-case, 5.08 cm worth of lightening 400 meters away will blow me off my feet. If the channel was only one angstrom wide, I would need to stand about 0.79e-5 millimeters away from the discharge.
Which is a fancy way of saying, it ain't gonna happen. The size of the vacuum (angstroms, at most) is so small that the "crash" of air wouldn't be heard by the superhero, much less anyone else.
But we're forgetting something!
Thunder is the sound made by the air refilling the vacuum from all sides,3 like hands clapping. You don't have that situation! At least, not until the superhero turns his superpower off. Until then you have, for example, air, rushing in to be obliterated by the danger zone! Woo-hoo! When your superhero turns this power on he quickly becomes the center of a tornado with air rushing toward him as fast as air possibly can under any terrestrial ground-level conditions. And it doesn't matter how small the area of his skin he involves in the superpower! It's like punching a hole in the side of a space ship. "Bad Things Happen."
The obvious consequence is the lawsuits filed against him for all the property damage and death (oh yeah! Death!) due to people, places, and things being sucked toward him at beyond hurricane-force wind speeds. And, of course, when they come within 2cm of him, they vanish (in neat little atomic slices!).
But those lawsuits aren't really a problem because, unless he has super durability (like, Superman level super durability!), he's dead the moment he shuts off his superpower. Because that's when all that air/matter/stuff/people hits him at more than the speed of sound. Being dead, he won't hear a thing.4
But the "bang!" it would make would be heard the proverbial hundreds of miles away.
1 Totally unrelated to the question is the reality that anyone reading that quote and then thinking about the fact that the channel is pure, unadulterated electron flow should now be peeing their pants. It's a good example of why Mother Nature usually wins.
2 I don't actually remember the sound of thunder, I do remember having all the wind knocked out of me. I don't recommend experiencing this.
3 "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." (Source) Yes, the development of thunder is more complex than described in the text, but not much and it's beside the point — you still don't have that situation.
4 Let's look at this from opening only a dime-sized area (2.5 cm) rather than his entire body surface area. the world-record tornado wind speed record is 301 mph or 134 m/s - and that wasn't sinking air into a vacuum. I found a calculation online for a 1 ft square hole (929 sqcm) that suggests roughly 1.74 SCFS or 49.3 l/s for a dime-sized area. People standing next to the SH and the SH himself are in danger, but the force is dispersed quickly with distance. However, when he deactivates his power, the force of impact will break bones and potentially punch a hole in his hand (it depends if anything other than air is being carried by the wind). While active, the dime-size hole will try to pull his hand with the same force as the force of wind being sucked toward his hand (Newton's 3rd law), which is going to dislocate his shoulder and drag him around like a wild fire hose. This guy can get very hurt playing with this superpower.