There is a chance of survivorship bias. You get a bunch of messages through the chat interface and all of a sudden you believe it adds value, when in reality you're potentially annoying a whole bunch of users that aren't necessarily telling you that they're annoyed.
A favourite story[1] (and I can't remember where I read it first) is the WWII bombers that the US military were trying to understand how to protect by analyzing the bullet holes. But the bullet holes only told part of the story. Any bomber that made it home to be analyzed had only been hit in a non-critical place.
I'm not saying there isn't a place for chat, because I believe that they're absolutely is. A good, direct to the person chat, or unobtrusive ability to reach out is great.
Shoving it in my face and breaking the flow of what I was doing is not.
While I agree that HN readers aren't representative, I have a hard time believing that other people don't behave the same way when presented with annoying website behaviours (even if they later want the contact with the human).
I've seen behind the scene of businesses that get customers asking stupid stupid questions, so I also understand the where the zendesk 'are you sure this doesn't answer your question' comes from. Doesn't make it any less annoying when applied badly to expert audiences.
[1]:https://en.wikipedia.org/wiki/Survivorship_bias