Well, as long as the interest in the mods are still there, we will just continue playing them as usual. The difference between the gameplay would be the biggest thing I see, but I don't think that modders are going to worry about porting their mods to BCoF.
Lets consider what mods are in development; The Zombie Mod, Iron Europe, and the Boshin Ji Hietai. I don't know much about modding, but these games look promising. They will be modded with the NW coding and played that way.
Don't take offense to what I'm about to say; I don't think, and I'm sure some people agree with me, that all these mods probably will just be played casually. I don't think Iron Europe battles will be too common, just because gameplay will be a bit slow. Zombie mod will be a good game to play on the side with some friends, and I don't know a lot about the Boshin mod.
NW and N&S communities will port themselves to BCoF when it releases and the mods we come to love will most likely remain played as usual on the NW engine.
Just my opinion though, don't flame me!