In reality it makes no difference where the heat pack goes as your main concern is the heat loss through conduction through the insulated box resulting from a temperature differential. There should be little to no air in a properly packed box and it should also be air tight. The heat loss will be the same regardless whether it's placed on the bottom, side or top. If you're attempting to make free convection flow patterns in your shipping boxes then you're doing it wrong. The temperature in the box and the bags of corals should and will eventually be the same during shipping. Heat packs do get hotter than safe temperatures for livestock so direct contact of the packs and bags containing livestock is not recommended. BWA is correct, the bigger issue with shipping is actually too hot, not too cold.
They are placed at the top simply because it's the least likely place to get wet. 9 times out of ten the bottom of shipping boxes arrive wet or flooded. No other reason, it's just common sense.
On a side and completely unrelated note, three types of heat transfer exist, advection is just a form or convection (forced convection). Radiant heat transfer occurs in all objects provided there is temperature difference, so a heat pack certainly does transfer heat through radiation.
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