Its worked just fine this way for 10 years. Is it actually broken now and worth fixing, and further, why devote the energy when it continues to work fine? And really, the last thing HN needs are giant tangent comment trees. These rarely remain professional and on-topic.
From what people have posted, I would argue that the "threads" link is a failed attempt at something nearing notifications. I literally never clicked it until today after years of using HN. At some point, someone thought it was a good idea to implement the tracking of all the conversations you participate in. Why not try to make it more useful? I think the suggestion for "threads (12)" is great. You can't possibly think that makes things too complex?