In my experience, it does matter. I use both method depending on what am smoking, what coals and whether i have the mood to move them around all the time.
When using shiny side up, i dont need to move the coals all the time around. It also works much better with a windcover. If am not in the mood to play around with the coals i put it shiny side up and just plop a bigger piece of charcoal than normal and it works like a charm.
Shiny side down works better with glycerin based stuff (eg. fusion, starbuzz) and makes bigger clouds to the expense of shortening the session. If you can get 1 1/2 hour from fusion with shiny side down, you can probably get 2 if you put the shiny side up and a bit more heat.