The air box is an integral part of the the bikes fuelling/induction system if you remove it everything becomes a trade off regardless of what jetting you do and it's not just jets, needles will also need adjusting or changing to get some of the drive back not to mention dyno time. Sure you can just change the mains and it will run of sorts but it will not be running at optimum, fuel consumption will rise and it may well improve the induction noise but that's about it.
At large throttle openings you may well improve things slightly (I mean slightly) mid and low range will suffer, as will torque in the low to mid range not to mention poor wet water performance.
Think about it the bike is a late 90's design producing at the crank almost 100bhp from a 600 early 90's 1000/1100's were not producing much more out of the crate. Air boxes are one of the ways of getting high output with good manners, name a modern bike that doesn't have one, most sports bikes employ ram air or pressurised air box/induction tracks.
The Fazer engine is already highly tuned as standard there is virtually nothing to be had with old school tuning tricks open carbs, stacks and individual filters as a way of gaining a few bhp are a thing of the past this side of a drag strip.
What works and gives you 1 - 2 bhp and improves the low to mid range is a K & N and a can fit and enjoy.