You realize that your factory hood had functional vents that leak water too, right?? Just like Kevin said though, as long as it's not going onto the filter, you'll be just fine.
Isn't that the entire point of a hood with heat extraction vents. Every GT500 hood has a hole that "leaks water in to the engine bay through a hole". Every Lancer Evolution has a hole in the hood and so does the Aston Martin V12 Vantage, in fact a large portion of it's hood is essentially open to the elements. I don't see what you're so worried about. Trust me water makes it's way into the engine bay through the radiator as you drive in the rain anyway.
I'm sure you could fab up some sort of "block off plate", but then you're disabling the usefulness of the vents.