The stock Honda CRF450X airbox is safe from water, but it's also safe from air. If you make vents in the proper places, you get good results without problems from wet air-filter elements. The secret for more free airflow is using a small piece of 2.5cm steal pipe, every D.I.Y. Shop has it, heat the pipe over a flame and then poke holes.
The holes come out looking like they belong there. Just try not to burn a hole in your fuel tank and make the Honda CRF450X burst into flames.
The snorkel has to go. Use a drill to handle the two rivets that hold it in place. We put four holes in the the areas that are protected from splash by other pieces of body work. It's not a good idea to have any holes near the bottom of the airbox.
After the snorkel is gone, you can vent the top of the airbox in a number of places. Water isn't an issue here; the reason the CRF450X comes this way is to eliminate suction noise.
Once you get more air into the engine, you need more fuel. An NCYS needle in the center position with a 150 main jet will feed the Honda CRF450X perfectly.
The only reason to remove the air injection system is because it's so ugly. It doesn't affect performance, aside from perhaps a little backfiring. But if you do remove it, don't just plug the holes and leave it like that. Use some legitimate removal kit to fix the hole...