Its hard to drill the baffles out because you have to cut and weld the muffler back together but it doesn't hurt a thing if you do it. I've done it to a few other atvs and bikes, it helps keeps the muffler cooler and if you stick with the same size muffler outlet it has no effect on how it runs.
Are you sure removing the air box resonator made a difference other than how loud the intake noise is? All it does is lessen the noise you hear from the air box while riding, it doesn't improve air flow into the air box at all, the air still has to come through the same size snorkel.
