Go to a craft store and get some dense foam for upholstery and cut some foam plugs for the scoops. You can even paint the outside black. That will help seal the foam and sorta hide it too.
Really not necessary. I’ve had the hood scoops on my car for quite some time and have driven it in absolute downpours, the hood scoops aren’t an issue. You’ll get more water splashing in from the bottom and through the grille than through the hood scoop holes.