Nah, you did the right thing. If anything its taking in cooler air from further forward in the bay. The resonator box connector you removed had a very high intake position up in the engine bay. I ran with a K&N panel filter and the resonator pulled for a long time. I got better throttle response but not much else. Definitely worth doing, I think, and its basically free.
What you should do is leave the pipe attached to the front of the air box and remove everything underneath it. Leave #8, the elbow pipe out the front of the air box and the section below it. Saw off the box at the bottom and you effectively have a CAI that can't hydrolock.
Heres a pic: Leave #8 and the section after it. There is not number on it but the section from gasket #10 to the box. Cut it off at the box and BAM! Free CAI. That is what I would do. If you removed #8, put it back and get rid of the rest but it sounds like you have already noticed how much better it is with the rest of that crap gone.