By baffle what do you mean? If your refering to the baffle packing (usually fibreglass/woven heat proof stuff) then you shouldnt see an increase in performance. Removing the baffle will mean exhaust gasses will travel thru the perforated tube in the muffler slowing their velocity giving more back pressure.
if your running a 4 stroke it isnt a good idea too ride without the baffle and exhuste off it creates less back pressure and can screw ur bike had porblems with mine
sik, on our 29s that cone shaped screen is the spark arrestor. If you take it out the bike will run better but be careful where you ride, don't want to start a fire...most other bikes that I have seen do not have one anyway.