Injen also made the box type air box. It basically just removed the top of your airbox, added a conical air filter, a silicone hose to the throttle body and then you attached it to the bottom of the airbox. A really good upgrade for it was to use an SVT airbox bottom with the SVT snorkel. They came in colors of black, silver, blue, red and yellow.
Bypass valves are effective for doing what they need to do. But you have to make sure you check it often as something may get lodged in it and keep the valve open allowing particles to come inside through it. That is not likely to happen though, just an extreme possibility. Most of the by-pass valves have a sponge filter around them though to prevent such things. And for what it's worth, it is very unlikely that you would suck up enough water to do any damage to your engine through a CAI anyways. In order for you to hydrolock, you would have to literally dip the entire air cone into the water to even get enough water to damage the motor.