I think I heard that they used CG somewhere. I went back and compared some scenes from Nodame and the Allen playing piano scene. The songs played in Nodame are much more complicated and the CG suits it since they're fast and hard to animate normally. Yes, they do use the CG for the other instruments as well. It doesn't really look "fake" as much as it's a lot more realistic than everything else going on so it doesn't quite match, but it still looks good.

Allen's scene was for a much simpler song, but considering the genre of the show, it is admirable that the studio paid that much attention to the movement of the fingers. It really does match the music, however simple it is.