Depth is an extremely important factor. Light has a hard time going through water, which is why it gets pretty dark pretty quickly when you dive in the ocean. In terms of our tanks, I'd say it has two primary impacts:
1) The higher the light source, the more spread you will get. In other words, it will cover a greater area.
2) The more depth the light has to travel, the less light will penetrate to reach your corals.
I do believe the height difference you reference could make an impact on a coral's growth and coloration. I've heard many of our most successful reefkeepers reference how moving some of their corals just a few inches made a tremendous impact on either their growth rate, coloration or overall health.