Yes. That unfortunately leaves the harder questions of what to do with flagged comments and faded comments. These signals are extremely important for calibrating users' perceptions of the community—especially new users.
I can understand removing dead comments because they tend to be more accurate in terms of what the site isn't for but faded comments definitely have mixed signal to noise ratio. It may not be evenly split but it's somewhere around 20:80.
Oh I don't disagree. But the fading is an important element of HN's design—I don't mean its web design, I mean its community design. It's one critical way in which the community signals that it has found something wrong with a comment.
I know that downvoting is controversial and I know that the fading feature is unpopular with some. But it is the way the community works. We can debate it at length and I'll argue that it's a good feature. (I think it was one of pg's master strokes actually. For all its annoyance, it creates important feedback loops, both within the community and between the community and the outside world.) But the point here is that since third party clients are representing HN to the world, there's a need to represent HN as it actually is. Otherwise readers come along, get the wrong idea, and judge the community badly.
To be clear, we don't supply the fading information in the API yet, so third party clients couldn't represent this aspect easily even if they wanted to. But it's an example I've started to think about lately.