The only reason the whale was taken off NRT was because they started HND and they knew all the pax would go for that flight because of the proximity to the city... no airline would continue to operate an aircraft on a route that had no traffic.
Every NRT I ever flew was full to the brim. So the 380 was ideal because the loads supported it. That has now changed since a more convenient route has opened up. I don't believe it had anything to do with any "shortfall" of the aircraft on that particular route....