I cut holes in all of my bodies. (all I have is off-road) It helps cool the engine, and allows access to fuel door, so you don't have to take the body off to refuel. As far as protetction for the truck, as long as you don't cut them too big, and try to stay 1/2 inch from any corners, it shouldn't compromise the integrity too much.
If you are running in very cold weather(below freezing), you might want to cover the holes to keep some heat in.
It has been my experience that dirt, mud, snow, and everything else that you drive over/through, WILL get inside the body, and all over your stuff. The best advise is to protect each individual component.
And if you run in the snow, be prepared to do alot of bearing maintenance. Especially if you run on any sanded/salted snow. That stuff will make short work of bearings.
Use a temp gun to monitor temp in cold weather, and if you need to, wrap the cooling head in a sock or foil tape to keep temps over 200 degrees. Be cautious of leaning the engine to get the temps up, as you could fry a piston that way.
Good luck and have fun, and if you crash really bad, take pics