I think most people who would shoot with a D90 would not care/know how to hack the firmware to reset the count. Here are some observations when buying used.
Are all accessories included? This gives a general idea of how a person cares for their equipment. The worst used cameras I have seen, they typically are sold body only with the battery and maybe a generic charger from losing the OEM. Someone who has the box, and all the paperwork (receipt included) including the hot shoe cover / viewfinder cover seem to take better care of their goods.
Age, then shutter count. A camera a year old with 10,000 clicks might be worth more than one 4 months old with 50,000 clicks.
Ask for a sample shot of the sky @ f/22 focused at the minimum focus distance of the lens. You will probably see some spots on the sensor from doing this. How much dust it has on it can give an indication to how much use it has, or if the person just has one lens or not and never changed the lens. The sensor is worth more than the shutter anyway.