There are no aftermarket tuning options I'm aware of yet other than the Ducati Performance Up-Map that comes with the Akrapovic exhaust. I'm sure Rapid Bike and the Termi T800 will be available at some point in the near future for those building race/track bikes who need tuning options for various race exhausts.
There are always potential "warranty issues" with any aftermarket modification to your bike, in terms of if you make a modification and it directly causes a problem with your bike, you can not count on having warranty coverage for that issue. Ducati Performance factory modifications that are installed by an authorized Ducati dealer carry a specific 2-year warranty in addition to the factory warranty on the bike itself. Anything outside of that "can" have warranty implications depending on specific circumstances.