KennyBoy: I believe your original question was about light penetration in relation to a smooth water surface.
If we take a look at intensity reflection models, then we see that the reflection of light is maximized on smooth water surfaces. The more light that is reflected, the less that is penetrating. So, I would conclude that surface agitation (which gives the light many angles to possibly penetrate) would optimize the amount of light that is reaching our corals.
I could be completely wrong; these are just thoughts.
I hope this helps answer your question.
To those who are talking about O2: I don't have a clue which method allows for more exchange (skimmer or agitation), but even with the lighting ideals behind I would still have surface agitation since I don't have a skimmer. If someone does know anything else about the O2 matter, please post; I'm very interested. Good discussion.