I think it has more to do with airflow. Since you're creating a temperature differential, the air will want to move up, and if there is another fin in that direction, it will be harder for it to move.

Some people claim that you actually get more heat output when you're running an amp well below specs. I don't know if that's true, and I certainly don't know if that's universally true. (Sounds like something that could happen with some cheap engineering to me.) I don't have the same brand of amp you're looking at, but mine is also installed with the heatsink fins running horizontally, and I've had no problem at all. It just doesn't even begin to run hot enough for it to be any concern.