I don't see why the heatpipes won't work... heatpipe is meant to carry the heat from the small circular base to the fins, and the fins are cooled by the fan.

Energy transfer is CPU->base->heatpipes->fins-> fanned into the air

But of course heatpipes are only to help facilitate the movement of heat from the base to the fins. I dont see how it's wrong though... doesn't matter that no air passes over the heatpipes Alexio, they are meant to move heat as stated above - you don't need air flowing over them.