Not that it is highly relevant here, but the 2005 GTOs were also available to option to the flat hood instead of the hood with scoops. Twelve cars were built this way. I'm going to guess those that still exist probably have had 05/06 hoods swapped onto them by now though.
No clue why anyone then or more recently would have opted away from the scooped hood. Maybe back in the day they had plans to cut a hole in the hood for a big intake or a blower and though it would be easier to cut a flat hood than a scooped hood. Or maybe they just like the look better. People are weird sometimes.