This is a really good point.
I thought for a second that maybe the remote had gone Bluetooth, but there would be no reason to do so: Bluetooth sucks down battery life, and IR's only limitation is that it requires line of sight. Since you also need line of sight to, you know, see the movie that you're currently playing in Front Row, Apple is unlikely to consider this a problem worth fixing.
So yeah, I agree.
Errr...
You realize that if you're running front row it will be open. So yes, the IR eye could be in the black screen bezel. After all, what use is it to have a remote for a computer that's asleep?