The only place I really miss having them is in older articles and on searchyc.com. I feel a much greater compulsion to engage each comment on its merit when voting and when reading, and I feel like reading HN has become more intellectually stimulating.
However, this is more of a problem when I'm trying to assess information in areas that I'm not already familiar with. If I'm searching for information on which DNS providers are best and I find an Ask HN from 4 months ago, I can no longer tell what the true community consensus on it is. I expect the current masking of comments will provide less biased voting, so I think displaying comment scores on stories that are more than two months old would eventually provide the best of both worlds.