I don't know if it really matters in the context of hookah smoking but heat is transferred in three different ways. The first one is conduction, i.e, through contact of the of the coals with the foil. The second one is convection, where the heat is transferred through a fluid medium, in the hookah case, this is the air between the foil and the tobacco. The final one is radiation, where heat is transferred as energy by electromagnetic waves. If you look into thermos bottles, you will most often see a mirror surface. In theory, the shiny side of the foil is just like the mirror in the thermos bottle and should reflect the heat energy back into the bowl.
So, even though I haven't tested it in any scientific way, I always put the shiny side of the foil down.
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