I was wondering if I will have to worry about hydro-lock if I removed the snorkel that attaches to the bottom of the stock air box ? Thanks in advanced

nope

As long as you don't get a cold air that goes down to the fender well, you should be okay. I got a k&n typhoon and I just had my motor screwed.

I had the TRD / AEM one and threw a rod. It's a very poor design, but after my issue (and Toyota not warrantying it), a TSB did come out to offer the 04-05 TRD CAI under warranty. Sadly the '06 is still not covered.

Stock airbox will be fine, but why bother? You'll get colder air with the snorkel than from the middle of the engine bay.