as for opening them up, go ahead if you like. the vents do aide in cooling the engine bay when its hot, but without an intercooler to feed, the scoop doesn't do a whole lot, except if you modify a MY00-01 to have a ram air intake. you can't on your MY99 because of the MAF sensor. basically, i leave mine open during the spring, summer, and fall and then close them during the winter when i'm actually trying to keep the heat in the engine bay.
If you look at the above links those mods will allow air in but keep out rain and dirt for the most part. I took real time temps under the hood and removing the plates keeps the motor cooler by washing air over it. As stated air comes in the scoop, and out the front vents. The second air box (aka torque box) will get heat soak after a while and raise the intake air temp. Opening the scoop keeps it cool.