I think Saix is only saying what he has to. It's true that the Organization must get rid of betrayers and from the info currently out it seems Roxas is a betrayer
I think there might be an epilouge showing clips of Roxas after Sora's awakening but I don't think he'll fight Sora. I think the final boss will be Riku woth the final cutscene being when Riku and DiZ put him in the simulated Twilight Town
i don't think Riku has a nobody. ansem captured his heart but it didn't leave his body, so a nobody could not have been created from his body and soul.