| Probably.
When you simply replace the stock exhaust cans with aftermarket slip-ons you'll get the sound of a performance bike instead of the exhaust noise mandated by the government. Also, carbon fiber and titanium cans will save quite a bit of weight (so take a rear ride height reading before the change so you can reset it after.)
You'll also get a slight reduction in exhaust gas back pressure so the engine doesn't have as much parasitic power loss when moving the exhaust out the pipes. You'll gain one or two horsepower, that's it. I may be overstating the case a bit here but the truth is that exhaust alone is seldom a bottleneck in power production. Generally speaking, the air intake side is more of a concern. If you can get more air into an engine it's a trivial issue to supply more fuel and consequently make more power.
The stock fuel map on the chip or EMU supplied by Ducati is designed to provide good fuel economy and good power delivery across the rpm range (i.e. no big mid-range power dips) while still meeting EPA-mandated exhaust emission limits.
In other words, the manufacturer's main priorities aren't the same as the owner's. Ducati's Eprom's fuel and ignition maps are compromised to meet specific noise and emissions standards, yet produce good fuel economy and accomodate variations in engine tune and exhaust systems with a margin of safety. So, you might say that they are de-tuned slightly. As owners, we're mainly interested in two things: optimum power and acceleration, so what should we do?.
Aftermarket Eproms are developed to extract more wide open throttle power on a dyno at the sacrifice of good fuel ecomomy; so expect to burn about 20% more, and forget emissions. Sometimes this approach results in an undesireable mid-range power loss (where we do most of of our riding) so the red-line power improvement seems even more impressive to a seat-of-the pants dyno.
The truth of the matter is that most chips that are offered for aftermarket slip-ons (Ducati Performance chips included) simply increase fuel volume delivery by 3-5% across the rpm range.
If you want a better result than that you first need to get your bike tuned properly (including getting the cam timing set) and then, and only then, use a programable chip or Power Commander and a dyno. Bring money.  | 
Shazaam!
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