Exactly. CAI generally have the filter element mounted lower in the front or in the front fender area of the car where it is more susceptible to ingesting air. There are a couple of ways to combat this:
1) Bypass valve - some mfgs of CAIs have a water bypass valve, but this may not be completely effective.
2) Some filter elements, such as the ones by K&N, need to be oiled. In applications where there is more moisture or water, they recommend applying more oil to the filter element itself. This would help reduce the likelihood of inegesting water. However, it won't help if the entire filter is submerged.
3) Some people convert their CAI into a short or warm air intake during the winter months. This relocates the filter element back up into the engine compartment where there is much less likelihood of water ingestion. The trade-off is less power as the air temps underhood is much greater and there is also some loss of power due to the shorter piping (some of the better CAIs have tuned pipes which alone can increase torque/hp).
FWIW, I used to have a twin turbo 300ZX which had dual cone intakes located right up front near the mouth of the front bumper. I never had any problems even when driving in the rain. Of course, I exercised caution and common sense and never drove through deep pools of water.
