When it comes to heat transfer, "shiny" only effects the radiative third (least significant) of the equation. Conductive and convective heat transfer should account for 95-99% of the heat in your hookah head. I can't believe that a potential gain or loss of 1-5% heat can effect the tobacco cooking process in a way noticeable to the smoker.
That said, setting up the hookah is somewhat of a tradition, a process of lovingly followed procedures to achieve the perfect results. Some people believe these results are
improved by putting the shiny side down, and who am I to tell them they are wrong. I can't tell the difference either way.
I generally use 2 layers of regular foil rather than HD. I take 1 rectangle strip and fold it in half, giving me one shiny side up and one down. If there is a "correct" way to do it, i've got both all in 1 setup without trying or thinking about it (i guess if i fold it with shiny sides facing each other i've got neither... but i really don't think it matters).