If you dont want the scoop to go up with the hood, you could get the scoop mounted solid to the motor and cut a hole in your hood to clear it. It would be more like a rumble scoop. Then like you said you can use weatherstripping to seal it to the hood, ya just have to get the height right so when the hood closes it seals tight. Just an Idea
And for keeping water out, you could put a hole somewhere in the bottom of you intake tubing, and put a resivour or catch can there, so most of the water should drain into that.