The GT500 hood will leave a funny gap on your 2006 because of the difference in the GT500 front fascia.
As far as water getting in and being a problem with the open hoods though everyone has said it isn't a problem. A friend had one similar to the California Dream with the two big slots up front and never had a problem in rain or snow.
I have a custom set up with a shaker that is open directly to the engine bay. I've driven through some huge rain storms since doing it and no problems at all. In fact the top of my supercharger wasn't even wet.
with the hood up you can see it is a big opening too