I've been using his http://cheeaun.github.io/hackerweb/ to read HN on my phone for a while (is it years yet?) now. I try others as they appear and so far continually go back to his.
2. like most of the ios apps out there, there is no thread-level support. All comments are on the same level.
2. ??? Comments threads are collapsible and indented properly.
Are you perhaps not looking at it on a phone? Try it on an iPhone, it's great.