I drove 30 miles in a torrential downpour the very day I installed my single CAI, no problems, and I'm talking about having to pull over and stop twice because the rain was so heavy.

When I got home, first thing I did was pull the grille and have a look, because I too was concerned.
The filter was perfectly dry.

What I think happens is this : the rain does get on the front and top of the filter, but because of the increased density caused by this, the majority of the air is pulled through the bottom and back where it is still dry.
But then, as usual, I could be wrong.