We do support one level of nested comments in discussions. It means that you can reply to the top-level comments, but if you reply to a reply, it'll appear on the same level. This is the same UI pattern used in ProductHunt, Slack, and Facebook. This way we'll make sure there won't be tons of empty spaces on deeply nested comments.
We are working on a way to show a reference to the replied comment, meaning that we'll show the comment at the same level, but it'll show which comment it's replying to. This is not yet implemented but is on our roadmap.