From my knowledge there's 2 main versions of the Ninja the original, and second version which came with an upgraded set of "elite" foils around and a longer bow if I remember correctly around (2011). From what I've been told the elite foils greatly improve boat handling and make maneuvers much easier. Some of the later ninjas also came fitted with prototype rocket foils and some even have the production rocket foils.
As far as I know the controls and rigging we're also continuously upgraded, and some boats came with optional extras such as aero wing bars. Some of the original boats with rigging and controls of the same age, seem to go for around £4000-£5000, with the later boats with the rocket foils and newer rig go for £6000-£7000. Make sure to ask what exact foils are included, as they seem to carry the majority of the value in the package.
I reckon there will be a decline in the price of the older boats in the fleet soon, as the newer exocets ect seem to be getting increasingly faster with more boats becoming uncompetitive. However there always seems to be demand for the older boats as people want to get involved with the class. Hope this makes sense! If you any questions fire away, although I may not be of much more help.