I used to have a 1.9JTD with a "Spider" Tuning box fitted for a while. I had no issues with the box itself and there was a perceived increase in power. It does screw with the fuel consumption computer though and tells you that suddenly your car is more economical, yet faster - great stuff if it were true (it's not)
After 15,000 miles the clutch was showing signs of slipping (box fitted from 22000 to 37,000 miles) and I sold the car very soon afterwards. I know the 2.0JTDm gearbox is stronger than the 1.9 but I'm not sure how much better the clutch is?
Remapping will be better than a tuning box but not always possible to do on a leased or company car, so tuning boxes still have a place.