If you've made the decision to ride it with the baffles in then dyno it that way, if you've decided to ride it with the baffles out (my choice!) then dyno it with them out. if you're not sure or may need to put them in from time to time do it as ktmguy says, for the reasons he says. As far as HP goes, it _should_ make more power without the baffles, a dyno tune will optimise the fuel map for your chosen set up. how it behaves today, with a map for a std bike, it would be hard to say which way will run better, but numbers mean little on the road, it's how it feels and rides that matter in the real world of day to day use.
paul.
ktmguy, how's life on the big island mate??