if i take out the baffle will it effect my yfz's performance and mess up the quad?  

From what I've read and experienced, taking your baffle or packing out can cause power loss. The packing helps keep the exhaust coming out straight and faster than without. The baffle removed will burn up your valves due to no backpressure. Either way, go with an aftermarket pipe and the proper jetting and you can't go wrong.  

taking the baffle out of a quad will usually cause you to lose horsepower and the only thing it helps is it makes the quad louder  

Just to give you an example, I found that my Big Gun exhaust had the packing removed. I repacked the pipe this weekend (packing available at any dealer) and the difference is dramatic. Not only is the sound more crisp, but there is no hesitation, and the Raptor went from being bad to a monster.It's not as loud as it used to be, but the power gain is worth a little decible loss.