First off, the filters don't sit in the bottom of the cover. I think everyone is forgetting that kn,
injen, diy.. all except JT have an exposed filter. Rain water always gets in the engine bay when it rains, so it isn't hurting the car. You will 100% not hydrolock for that tiny bit sitting in the bottom. I'm telling you from experience. We tried to blow up a car this way. Literally spraying a hose at an exposed filter, while revving the shit out of it for 10 minutes.
I wash the shit out of my car and haven't seen water collect there but maybe I'm lucky and other drips away from the shield. But I do agree it's trivial and dremeling a hole is a simple resolution.