1. Nation threads are good for minor news and other material not worth a full thread:
Not everything is threadworthy, although some users will likely disagree. Because of this, the Nation threads provide a place to discuss things that don't really have a place anywhere else. Want to make a comment on an exclusive that came out four years ago? Say it in the Nation thread. I know that I tend to miss a lot of topical discussion because I don't buy games upon release and because of that, I often find myself really wanting to talk about games after everyone is already done talking about them. This happened with Far Cry 3, and my laundry list of complaints with that game, and at the time, I posted it in an open discussion thread (which was later locked due to being redundant...hm). I wasn't about to make a thread about this stuff, because I really don't think my opinion is threadworthy (maybe that is why I've made a grand total of zero threads on VGC). I like having a place to talk about this stuff without having to worry about finding a place for this kind of discussion.
2. Things that are truly threadworthy will get a thread:
I don't think this really stops mass discussion of larger points. If something is threadworthy, there will be a thread of it and if it is really worth discussing, discussion will move to that thread. I really don't think users are shy about making threads (with some exceptions), so I don't see the problem here. I will say that I am more experienced with Nintendo discussion, so maybe this is more of a problem elsewhere.
3/4. Insular Communities aren't due to Nation Threads:
I can agree with point 3, but I'm not sure if the general schism (pt 4) is due to the Nation threads. In the wake of The Order, I saw plenty of posts calling out people who weren't traditionally Playstation supporters as "haters" and whatnot. I think this is a problem, as it limits discussion and it tries to push away the "all opinions are welcome" nature of the Hot Topics forum, however, I don't think this really has much to do with the Nation Threads. While mini-communities do form in most long running threads (COMG, Anime, Rate the Song, Nation etc), I think that these are mostly positive relationships.
Overall, I don't particularly see them as a problem, although I also don't see them as really good for anything either. Yes, they are a good place for small news and discussion, but I wouldn't shed any tears over losing them.