I cut my hood scoop because I was bored. I really didn't see the point of having a hood scoop just for looks anyway so I tried to make it "functional"
Now that I cut it out, I think it looks better this way! I don't get much (if any) water in it because it's not my DD so I don't drive it in the rain. If you think that driving you mustang in the rain with an "enclosed" hood make it water proof, you're mistaken. It's an open compartment, there is no bottom barrier to protect the motor from the rain. In the summer time you can see the heat coming out of the hood cut out so there is some function to cutting out the hood scoop. If I were to do it all over again I would do it like the OP did and keep the grill and drill it out. It'll prevent the hood scoop from coning up like mine but I still like the way mine looks better then the stock fake hood scoop.