Old thread here, but figured I'd chime in since I'm running a functional hood scoop on my 2001. When I bought it, the previous owner had cut the back of the hood scoop off with a dremel, so it's fully functional now.
Pros: There is a DRAMATIC cooling effect. When you're driving around and you come to a stoplight, you can see the heat pouring out of the hood scoop (like the blurry waves you see coming off hot asphalt in the summer). If you put your hand in front of the scoop you can feel it too. I think this helps to lower the intake air temps a bit and helps with pinging (mine's supercharged).
Cons: All kinds of dust and other crap blows in through the hood scoop and deposits itself on top of the engine. Also, in a rainstorm or a snowstorm you end up with a wet engine. In snow and below freezing temps, this can be a big problem because you can get little pools of water in the low spots and it will freeze in there.
I purchased a part from toyota that effectively blocks the scoop (it is part of the OEM install, and one of the parts that was cut). I just put it back in today to re-block the scoop.
I'm not sure if I'll leave it in or not, but it's easily installed and removed, so I may just keep it in the truck and put it in whenever I want the scoop blocked, and leave it open otherwise.