recently I read about clunky noises on irregular roads at low speeds in the rear axle systems of ND's that Miata drivers report after 50.000 to 80.000 miles (about 80.000-130.000 kms).
The general info I gathered from those reports is that it could be attributed to worn out bushings allowing for larger play in axle movements.
Maybe this is also the case at NC's. You did not specify milelage of your car. I suggest a visit to "MX5 Onderhoud" workshop in Hattem near Zwolle. Niek specialises in checking and diagnosing suspension and allignment of MX5's and aims at restoring the super driveability of our beloved sports cars.
At a Mazda dealership replacing bushings only is not what they do, so I have read on forums. They want to replace the whole rear axle system at considerable cost. Bushings replacement only is a lot cheaper. Just have it checked at MX5 Onderhoud in Hattem to see if this is the cause of clunky sounds or perhaps it is something else.