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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.

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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.

I know that the amps are supposed to be well-built, I just don't know how much heat they will put out. What brand amps do you have? If 5 more people tell me they have their amps mounted in a similar way, I'll start to feel better! The amps will be open to the passenger area and not in an enclosed trunk, so I imagine they will get some decent airflow around them just sitting there.

I figure that the more resistance that is in the system the more heat will be built up, so I am going overkill on my speaker wire and power/signal cables to the amp. Is this off-base? Just trying to head off any heat or sound related problems before they become an issue. The Nakamichi stuff seems pretty high-quality (from what I've read) and is supposed to sound very good. I bought it because of the SQ but also because it's very understated and the head unit will be less of a target for theft since it looks stock.