Just look at the components on the bike. Magnesium wheel's, Gas charged forks, one-off hand-made V4 engine and street-going electronics, lots of carbon, titanium and magnesium as well. Dealers bought the bike for around $60,000 USD, which means Ducati had to make them for A LOT less. Honestly, I don't personally see how they could have. If you watch the building process (there are some great Italian videos on this) you will see volunteer staff from dealerships around the world, assembling the motors. You will see the assembly run by hand on specially built stands, all of which cost them a considerable amount of money to produce. Even if cost of goods and manufacturing was around $60k (which I feel is about right) that doesn't take into account making enough service parts to cover the 7 year warranty and it absolutely doesn't cover the labor fees dealers must charge for fixing them when they break. Desmosedici's are notorious for having blow-by issues and many bikes have been in the shops more then once for simple, but expensive engine service.
All of that to say, yes there is enough evidence to substantiate the claim "Ducati lost money on the Desmosedici project" which by the way, if you did a google search, you can find the articles which substantiate my comments.
Ducati could have continued producing Desmosedici's, but you may notice they haven't. That's simply because they learned their lesson and companies that loose money, will never stay alive. The Superleggera is already starting to have engine issues and it was just released. It's very hard to take a race bike and turn it into a reliable street going machine. I doubt we will see more of these from any manufacturer in the future, it's simply too risky.