Comments cannot be hidden by downvoting. Comments are marked [flagged] [dead] only after other users have clicked on the timestamp and selected "flag." I think that these things get conflated because comments that tend to attract heavy downvotes also attract flagging. The [flagged] [dead] comments are mostly (entirely?) killed by the actions of ordinary users, not moderators.
Comments that are marked [dead] without the [flagged] indicator are because the user that posted the comment has been banned. For green (new) accounts this can be due to automatic filters that threw up false positives for new accounts. For old accounts this shows that the account has been banned by moderators. Users who have been banned can email hn@ycombinator.com pledging to follow the rules in the future and they'll be granted another chance. Even if a user remains banned, you can unhide a good [dead] comment by clicking on its timestamp and clicking "vouch."
Comments that are marked [dead] without the [flagged] indicator are because the user that posted the comment has been banned. For green (new) accounts this can be due to automatic filters that threw up false positives for new accounts. For old accounts this shows that the account has been banned by moderators. Users who have been banned can email hn@ycombinator.com pledging to follow the rules in the future and they'll be granted another chance. Even if a user remains banned, you can unhide a good [dead] comment by clicking on its timestamp and clicking "vouch."