Ducati built the Desmo road bike to make money. They increased production from the original 500 units because of demand (they also upped the price). 1500 units @$50,000 generates a gross revenue of $75 million dollars the bulk of the development had been done in building the race bike, so the development costs would be far less than say building the new Panigale. So there was a very good margin on those bikes, which they didn't even have to market.Ducati announced the D16 at a time when the FIM was being difficult about upping the allowable twin capacity to 1200. My take is the D16 was a shot across the bow to the FIM and the four cylinder marques, saying either let me take my twin to 1200, or I'll bring this baby to the party. I think that's why Ducati produced such an unheard of number (1500) of a limited edition machine. At the time 1500 was the required homologation (I believe). Ducati certainly did not earn much profit on those bikes.
Once the 1098 was approved for WSBK, the D16 approach was no longer needed. Now here we are over 5 years later and Aprilias essentially got their own D16. Make no mistake, the folks in Noale pay attention to Ducati's moves.
Kudos to Ducati though, for sticking with a twin, and now developing it to amazing levels with the 1199. It will be interesting to see how the Pani fares against that rocketship Aprilia in Superstock this year (and WSBK in 2013).
Ducati would never have raced the Desmo in superbikes because of the embarrassment it would have caused when their "GP Bike" got beat by a lowly streetbike. Ducati's political leverage in superbikes has always been to prop up the series with customer bikes and using the threat of leaving for leverage. That is why it's latest maneuver failed, because they no longer prop up the series since it is now supported by multiple manufacturers.