It sounds like the author is concerned about the work version of the negative social network effects of modern technology - using it to maintain lower levels of communication (no body language, etc) with people you already know while reducing your "white swan" opportunities for increasing your network via unplanned connections IRL.

If you don't have an open office plan, though, I wonder how much headphones are really cutting you off from the office network? I guess the author is referring to layouts where you use headphones to cut out excess noise around you, which wouldn't be as much of an issue in non-open plans.

I like to use headphones for background music, but I keep it on the lowest level possible so I don't miss out on external conversation when it arises. I'm not sure if it creates a negative impression when I'm talking to someone with headphones in even though I can obviously hear and understand them; I've never been made aware of any such impression but I've also never asked.