Physical locations don't let me participate in massive numbers of discussions at once- I engage more fully with one person/group of people. And on HN, I can spend hours and hours here without anyone likely noticing, while people would notice that I haven't left the coffee shop. And I would likely need to leave the coffee shop to get something done, while HN can be constantly on the side of my screen.
Physical locations also tend to force me to engage back- if you say something I disagree with, I may not speak up, but my reaction (or lack of reaction) communicates to some extent what I think. Online, I could be annoyed by you, or happy that you think like me, or seething mad, and no-one may ever know if I choose not to.
I don't think HN is generally worse than physical interaction, but it has the potential to be. Social environments often have some moderating influence on participants, through social customs, lack of anonymity, and better communication through body language, tone of voice, etc.