Low-mounted CAI is certainly not good for any kind of mudding or puddle splashing.
My ghetto CAI is mounted slightly lower than an OEM one would be, but anyway, my Thermac might protect me partially. It gets intake air from a heat stove at the exhaust manifold and mixes with cold air to keep IAT at 115°F (except it switches to cold air when under 6 inches of vacuum), so it blocks off most of the CAI's flow.
I considered some sort of safety valve flap or drain in the CAI at a low point but I don't think it's necessary since my design is so similar to OEM.