Hi Robert,
I read the same thing while I was in the middle of doing an acts_as_nested_set forum implementation myself, and it did give me pause. But, since I was already going down that path rather than using acts_as_threaded, I decided to press on. I was able to successfuly use acts_as_nested_set for my threaded forum app, which I started yesterday and more-or-less finished today. I am happy to say that all of my tests run, and it seems to be performing well. My particular forum has multiple roots as well as multiple forums, and so far, I have not seen any problems.
The directions I followed were from Bob Silva's site I.nfectio.us, and here is the link: http://www.railtie.net/articles/2006/03/31/implement-acts_as_threaded-without-a-plugin
Bob is the author of acts_as_threaded as well.
Hope this helps!
C