When I started visiting HN around 2008-2009, if I am not mistaken, the website used no JavaScript. Anyway, in the browser I use, HN is "flat" threads, all posts visible and left justified, no indentation. It still looks just the same as it did in 2008-2009.
I keep JavaScript on, but I rarely collapse comments. I could probably browse Hacker News without JavaScript if I wanted to, because they've taken care to make most of it work.