My factory can on the 2011 BMW S1000RR is straight through, with the perforated pipe and wadding, as are just about every bike these days, as seen in Dave500's photo. I installed a Laser GP slip-on with removable baffles and removed the baffles. Sounded cool, but I had a fueling issue at around 3K that the Fuel injection could not compensate for. So, I removed the fibreglass wadding and re-installed the baffles. It is a little quieter, but still sounds good and fuels correctly without me going the PowerCommander route.
If you are running straight pipes on a carb'ed bike, and you are running factory jetting, then you are running lean. Especially if you are running the stock airbox. This leads to all kinds of problems, such as running hot, and burning plugs and piston tops, and cooking your oil to ash. Are your headers a real dark,deep blue at the head? That's one sign of running hot(but other conditions can cause that).