Water will ALWAYS get into a CAI when it rains. It won't hurt the engine in the least, though. It's when you drive through a huge flood with water more than one foot deep is when you should start worrying, since the water will envelop the filter and turn the CAI into a straw for the engine.

During rain, downpours, hurricanes, etc., you don't have to worry at all unless you don't have your undercar plastics and drivers side wheel well on. That would allow a ton more water into the CAI, enough to start pooling up and eventually close off the piping completely. Then the car will hydrolock. A heatshield will help lessen the chance of that, since it wil block the excess water hitting the filter.
BTW, the bypass valve doesn't work on any Celica intakes, and make sure you don't overoil the filter, or you'll roast your MAFS. Just lightly mist the filter. The oil will soak in by itself. Then drive the car hard for a few min (sucks away any excess oil) and clean your MAFS.