I'm not sure what to do about this, but there are increasing signs that it's a problem. HN is what it is because it has a specific, opinionated, highly intentional design. It's fine to disagree with that design—plenty of users do. Probably every user does in one way or another. What's not fine is for third party clients to break this design in a way that alters the community itself.
There's also the fact that some apps are now charging money, which feels to me like a violation of HN's spirit, which has always been to be completely free. I like to say that the currency of HN is curiosity, not money, and we'd like to keep it that way.
We may have to produce some sort of standards for HN apps, which is a drag because that sort of bureaucrat is the last thing that any of us is interested in being.
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.