The risk/chance really depends on 1.) the car and 2.) filter location. All it takes is a dark, rainy evening coming home from work, and a street drain completely blocked with road side tree leaves.
That was the scenario I was in over a year ago with my RSX Type-S and CAI. It was too dark and rainy to tell that the road outside my apartment was flooded with about 4-6" of water. (I've come back after many rain storms and never saw a flooding problem there.) I drove over the water at about 25mph, splashed water all over my front end, and sucked in water thru the intake to the point where the engine basically was about to stall as I quickly turned the ignition off. I sat there silent in the middle of the street thinking, "Oh s***! Tell me i didn't suck up water." So, probably the dumbest thing I did next was turn the engine back on because I didn't want to push the car standing in 6" of water. Car sounded like s***! Just kept sputtering and wanting to stall. I eased the clutch enough to get moving to the curb and parked it. I ended up pulling the spark plugs and covering the holes with a towel to let any water that might be in the combustion chamber evaporate over night just as a precaution.
The next morning I changed the oil, which was milky brown due to the water in it. I probably dumped about 4 qts right thru the oil pan after draining it just to filter out as much as I could. Filled the oil, popped the spark plugs back in, fired it up, and it ran like s*** and smoked white like a bastard! I thought the motor was shot for sure, but I took it around the block anyways. After about 5 miles of driving, the smoke and sputter cleared up, and the car was back to normal. I changed the oil 500 miles later just incase I didn't get the remainder out. Close call!!
Note that the filter was generally in the same location as the MS3's CAI - front left. Although I did have tein ss coil-overs, so the filter was probably closer to the ground. What actually happened was the plastic clips holding the plastic underbody panel on to the front bumper came apart and actually "ramped" water up into the filter. I don't think the MS3's configuration would allow for this to happen as easily though since I believe its got 3 bolts along the bottom front bumper's corners.
Overall, I think the CAI for the MS3 is designed better to prevent sucking in water with both the splash guard, and that the filter is consealed behind more plastic panels. So I'm not bashing it. But like someone else stated, be prepared for some instances where something can occur. Just use common sense and be precautious when they do happen.
