Well, I have been here for about 1.5 years so my experience is on this is lacking but from what I gather, Nation threads are great because, as like you have said, its a "safe heaven" for fans and imo, that positive outweighs its negatives.
Cause imo, if a person says, I love the wiiU over the ps4 for blah blah blah or I love a vita of the 3ds cause blah blah blah, in a Nation thread, chances are (as long as u are in the right thread), you won't get attacked and a lot of people in theory, should agree with you! Where as if you did that via ur own thread, you would probably get attacked as well as other things for better or for worse.
Same logic also applies to software. If someone prefers Digimon on the vita over Pokemon on the 3ds or XCX on the wiiU over FFXV on the ps4/x1, in a Nation thread, people should agree where as if you made ur own thread, then it may not turn out so well for you.
So I guess what I am trying to say is, Nation threads are great because they let people with similar tastes meet in a predictable and safe* environment which is very important, specially for newbies! And since the Nation threads are so big, a lot of the people probably don't comment on them or check them if they have no interest on the blah fanbase where as a new thread = more people commenting regardless of interest even if they are in the blah section, if that makes any sense.
So yea, I think we should keep them and they should continue to exist! Even though I visit one like once every 4-6 months loll
And honestly, there are plenty of other things that need to be improved/changed if we want the community to grow that should come wayyyyyy before the Nation threads. I think the Nation threads are the last things that we need to worry about when it comes to "growing/shrinking the community"