I think the three main reasons Sports fetch more than GTs are:
1) When new, Sports sold for a bit more than GTs in the first place.
2) GTs were available for two model years after Ducati dropped the Sports.
And finally, (drumroll here),
3) The cafe racer craze.
Bottom line though, GT prices and demand are on the rise. I regularly check what people are getting for them, and even older, higher mileage ones in good shape but stock or close to stock condition generally go for $7,500-8,000. Just two years ago, those same bikes probably would have only fetched $5-6,000, even with fewer miles on them.