So I'm chiming in on an older thread but a couple of things to address from my background with aerodynamics to help shed some light here.
1st - The 99/01 Cobra hood that ended up on the 03/04 V6s is not functional at all. The 'vent' isn't open. It's just like a backwards version of the 'scoop' on the V6/GT from 99-04.
2nd/3rd (two points tied togethe) - Old school cowls (and NASCAR) work with carb'd set ups. The vent at the base of the windshield sucks air in - giving cooler fresh air to the top of the motor. Also, having the carb up top creates vacuum at the top of the engine bay, which the newer cars don't have. If you want an example of this on a fuel injected Mutang, look at the Stage 3 Roush from 1995 for the 5.0L. Relocated air inlet/filter at the top of the motor toward the rear - and a matching hood with cowl vent at the back which created that sweet spot for suction. Nice outside air pulled right in.
They Y2K R hoods with vent on the top that are open work very well for heat extraction due to the nature of the air flowing over that point of the hood. It would have been more function to locate them further forward and wider - like the Terminator. The Y2K R hood also takes into account over all airflow coming off the hood and transitioning it to the windshield. It's working in harmony with the splitter and rear wing they are also equipped with.
The reverse vents (like made) help suck the hot air out after it passes the radiator. They work very well. If you try to force air in the top of the engine bay of the newer Mustangs you aren't doing anything of use. You are forcing air backwards from how it's naturally flowing, and creating pressure where you don't want it. Granted, it isn't enough the typical street car will ever see, but on the track - you'll know it.
You want hot air out as soon as it passes your cooling contact point (radiator). You also want it out over the top. Having disturbed air (or any extra air) under the car will also cost you on the track.