Like almost everything in the real world it's never as clear cut in every situation. Drive designs tend not to have any proper thought on cooling, as the makers don't see it as an issue. If it runs at 50C and lasts 5 years instead of 10 then so what....
The thing is they have to follow a size form factor, so I guess cooling fins at the top or bottom would be harder to incorporate in the design.
Things to remember, cooling the top will generally give you more surface area in contact with the block than the sides. Natural heat paths always favour rise, (upwards), but heat will tend to migrate to a cooler surface, assuming a reasonable thermal interface.
I have a Centrino laptop that runs pretty cool with the fan off, and in doing some disk ghosting of the 2.5" drives in my main PC I've been using another spare drive in the laptop. It's a faster drive but gets extremely hot in the laptop case. Just sitting a 1U P4 copper heat sink on the plastic case of the laptop above the HDD area helps soak away some of the heat. The copper 1U P4 sink gets quite warm and that's with an air gap, and at least 3mm of plastic to pass through.
Imo, better isn't always going to be the sides in every situation, it depends on many other factors, my Cuda IV's did tend to get hottest on the top plate, (probably due to heat rise more than anything else). I just can't see it matters where you cool HDD's as long as you cool enough of it's area, (excepting high performance SCSI HDD's may require a more specific design thought on cooling). I think it's much better to design it to fit your specific needs shape and size wise, while keeping in mind contact over a lager surface area should keep the complete drive at a lower even temp. Also important is that the design doesn't leak.......... that would kill your drive faster than any heat related issues
