I'm glad I saw this thread, because I thought of drilling mine out, too. Based on what I've read here, this is what I gathered; and it makes sense.
Picture it this way:
With the grill stock, the air is funneled through the opening which causes a very specific flow of air right through the middle of the radiator.
If you drill out the blocked openings, then the same amount of air (or more) will flow through a higher surface area, but at a slower speed and therefore, not go through the radiator completely. The air has to pass through the radiator to effectively cool the water; not around it.
I'm not sure if I did a good job of explaining it, but it makes sense in my head.

I'm keeping mine how it came from Ford.
Edit: The GT500 grills follow the same design as the GT/V6 grills. They are blocked off at the ends, too.
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'05 Legend Lime Mustang GT (Steeda CAI, UDP's, BamaChips 93 octane tune, ceramic headers, o/r h-pipe, FlowMaster axle-backs, 3.73 gears, alum. f/w, CHE brace w/ torq. lmtrs, UCA & LCA's, many exterior mods)