I think it all depends on where you ride. The spark arrestor is needed in most atv parks and national forest trails but if no one is looking where you are than go ahead it wont hurt. The air box lid is OK to remove if your not playing in the mud and the water. Its really there to keep the debris and moisture out so if you do remove it I would upgrade your stock filter to something like the K&N filter setup with a good pre-filter.
I'm still stock on mine took the lid off and it was just to loud but I do leave the spark arrestor out at least until i get the pipe I want no problems with anything except the arrestor bolts tend to seize up and twist off even with antiseize on them so be careful there.
If any of you have an old HMF tip around, it will fit the stock pipe with just a little hole reaming on the tip. The HMF spark arrester will work too. Flows alot freer and sounds better than stock, IMO.
If you know where the first baffle stops on the other side of the rear divider plate, you can drill through it with a long bit. The flow runs through 1 baffle back to the rear divider plate, then runs back toward the front of the silencer, then back out through the baffle that you can see. I have done this on a 400EX. On the 400EX is was 180 off from the baffle that you can see when you remove the spark arrester. It did make a difference on the 400EX with a filter a jetting, but it still sounded somewhat anemic compared to an aftermarket pipe.
you better have a very good air filter if you run without the lid, EHS makes a pre filter lid that gives you the best of both worlds. You need to have a better flowing exhaust system before you would benifit from any air box modifications.