I just bought a 2000 900SS in May, put it away about a month ago, and managed to log a little over 12,000 miles in the interim (about half of it over 12 days). I had 2 flat tires, one from bad luck, and one from stupidity and replaced the front, all told I'm into tires for about $450 or so.
I've hit two service intervals, the first at 600 miles, the second at 6,000. I'd say for the two of them my total was about $650 or so for the usual tensionings, tightenings, throttle balancing, and Ducati's ever perilous valve adjustments.
Since this is my first modern bike I have no idea what others are paying for service so perhaps my ignorance is my bliss.
For the record I am an engineer but I haven't taken it upon myself to learn the Ducati valve adjustment deal, maybe before spring.
As for reliability, I've never been let down, even on repeated days of 600 miles or more. I honestly can't imaging having a better bike for the way I like to ride.