When hood scoops were functional from the factory in the late 60's, there was always engineering to seal off water intrusion. Even the newer Mach 1 Mustang that reused the old "shaker" hood did so. There are two parts to consider. First, is keeping water out the the intake system. Second is keeping excess water out of the engine bay.
I don't think it will be a simple fabrication to add something in afterward. I would start by studying some of those old cars if you can find a way.