Ron,
I can't say that wet road dirt won't be a problem, but I did think this through. I collected stone particles, which had taken residence in my sills, when I removed them to put the vents in. I put the stones on the speaker grille, and it held 90% of them. I'm confident that the particles I may get won't be any worse then what I'm already getting. However, for insurance, I chose 1.5" holes because home depot has 1.5" rubber plugs that when shaved in thickness, fit the hole quite nicely. I'm sure 1.5" body grommets work as well.
I thought of the water too, and I can say with certainty that if you were to pour water directly into the vents, the water runs out the sill under the car. It seems the sills are sloped downward with some channels in them that the water naturally follows. I don't think water will be a problem.
I was hesitant to claim a substantial temperature difference without having good data to prove it. The weather here in Michigan has been a tad short of ideal, but when it warms up, I will put a few thermocouples on the sill surface and take temps after some controlled runs, with and without the plugs.
The theory of hot soaking is a common thought, but not really the worst case. The temps of the exhaust system are hottest when running high RPM's. At idle, the exhaust cools down. I can idle my car forever (about the only thing I can do in my garage in winter), and with the garage at 70 degrees (heater working O.T.) the sills never get that hot.
I do agree that airflow is the key to keeping the sills cool.
My observations. Stay tuned for actual data to prove or disprove.