No, washing it will not affect a cold-air setup. You literally have to submerge the filter in standing water for it to go up your intake. It's the exact same affect as sucking water through a straw. But all it takes is enough inches of water to go up to your bumper for you to be hosed (almost found this out the hard way with my Eclipse; had AEM cold-air but bypass valve worked like a charm and cut my engine out).

It's not easy to do with the ITR AEM intake, though. As you already know, since it's a single piece of pipe, you will have to cut the pipe in half... which leads to an even poorer fit