The only issue I have had with the 2.8JTD engine that has affected running is a broken electrical connection on the injector on cylinder 4, which a diesel specialist repaired for me.
I did have the Red Engine (MIL) light on for 70,000 miles (approx), caused by a 3rd piston deactivation in the fuel pump. This was diagnosed by a diesel specialist and didn't affect running in the slightest, due to the rest of the common rail system compensating! This one day, magically sorted itself!
My Ducato is used daily, so the electronics never get a chance to get damp, so I have had very good reliability over 5 and a half years.