I just felt that the holes are supposed to be there. If they weren't, Ducati wouldn't have taken the time to put them there.
Ducati put them there so any idiot can assemble their bikes. Just like they put yellow paint on some screws so a tech doesn't have to take out a torque wrench.
That being said I've drilled and cut off the nubs. Cutting them off is easier, but I did have to put a little tape on one of the controls. Not really a problem, plus when you decide to sell the bars there won't be holes in them.