With my 69 Mustang I have a shaker hood scoop--I drove it daily back in the '80s including through some of the worst downpours--never had a problem. Keep in mind--be it a shaker or a air box/plenum sealing to the hood you will still have an air cleaner and lid. The air does not go directly from scoop to carb unfiltered. I can't vouch for having the K&N filter lid, but with a normal solid lid the water should flow down into the lower part of the air box/plenum and exit through a drain tube. Whatever you engineer should have a means of draining any water that enters either through rain/snow/car washes.
on mine i am using a stock air cleaner base with a hi-po lid. i drilled 3 holes in the bottom of the base to drain the water, however this a very recent modification. i drove it for over 10 years without the drain holes and never once had a problem, even at the car wash.
The rubber seal that seals the scoop to the hood has a drain in it that runs down in front of the pass side cyl head. There is also a flap inside the scoop that only opens at low vacuum levels (like vac secondaries) so its only open when youre "in it". Otherwise the flap is closed and it draws the air from the snorkel (under the hood) like it normally would if there was no scoop. At least thats how my 70 is set up.
I have the standard '69 scoop that I've made functional, and I have an K&N filter top. Don't have any problems. The oil in the filter keeps the water from draining trough.
Whenever I wash the car, and open the hood, some water will run down on the filter, but it stays there. Then it vaporizes due to underhood heat when driving.
i've got the big arse Boss 429 scoop on my '67 with a ram-air box and K&N flow through top.
never had a single issue even in terrible rain storms. i've got a small hole drilled at the back of the ram-air box to let water drain, but i don't think it's even been a big issue.
at car washes i do stuff a towel around the filter somewhat just so that no excessive water gets in there.