Yes, that blocks some light and disperses the rest. What you want to do is 'capture' the light and focus it downward into the aquarium. To do this, point the thin side up.
Is there a difference you could actually see easily?? Or do you think it could only be measured with a meter?
Because I have been using eggcrate over my tank for quite a while just to keep fish from jumping out. It's cut into 2 pieces, separated at the center brace. I never even realized there were 2 sides to eggcrate until I read this thread. So last night I check and see that I have one piece on wih thin side up and 1 side on with thin side down (they HAVE always been used in the same orientation, because certain sections cut-out for equipment necessitate in which direction the eggcrate can be placed on).
I have never noticed any difference with the light on the 2 sides , and I tried last night turning them around (even though they dont fit perfectly) and still dont see a difference there either.