Your friendly Ducati dealer will re map the ecu for about £80.
My dealer said it really isn't necessary as the FI system will adjust itself a bit for a more open can.
There could be issues but the same issues as fitting any aftermarket can to any bike, how many problems do you know of?
Go for it, and if you're really that concerned get it remapped.

Fods

Cheers Fodder, its always the simple stuff that gets me confused:(

Gimme rocket science anyday
;)