Depends on what you mean by "they" and "fixed". There's a few clients. They do threading in different ways. I'm sure you'll find one that does what you like.

I mean actually threading the conversation. I.e. how hacker news does it.

I can't remember which ones, but I've seen at least 2 clients doing just that. There's also Toot! with its "subway map on the border" approach which solves the longer nesting in a different way.