like someone else already stated, the answer is...
Straight pipe: will, assuming re-jetting of the carb, deliver more PEAK HP than a baffled design. This really can't be debated, for 99% of setups.
Baffled Pipe with some back-pressure: will, for 99% of setups (there is always some exception that is simply a red herring), deliver more AVERAGE HP, and for sure average torque.
So, for drag racing purposes, where basically only peak power matters, or a very narrow RPM band, a straight-through design is best. For applications such as street, and assuming two otherwise identicle bikes, the one with some back-pressure is going outrun the no back-pressure (straight through) bike.
The same principal goes for running a bigger CFM carb, or bigger/hotter cam. What allows for more air flow, likely underperforms when max airflow isn't present.