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.
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.