No, the SAAB 9000 auto gearbox isn't really that bad, to the contrary, it's quite good.
What do a Rover 248, Porsche 928 and 944, Audi 100, Audi 6 &8, BMW 320i-V8 and Alfa-Romeo 164 have in common with the SAAB 9000? First, they are all very fast cars. Second, they all share the same ZF-4HP18 auto gearbox made in Germany by ZF.
True, rebuilding an auto gearbox is expensive, but it's no more then a gearbox for BMW, MB, Jaguar, Audi or Volvo.
That said, the life of the ZF-4HP18 auto gearbox depends on religious maintenance and fluid changes at least at 60K intervals or annually.
My '94 9000CSE has 189K and the ZF-4HP18 autobox works perfectly. Use Dextron III fluid.
So if you fancy a late 9k CS with an auto gearbox, take it for a good road test and check that the gears shift very smoothly with no thump or hesitation. Try it both cold and hot. Check for leaks from the transmission, these are costly to repair. As far as the manual 5 speed gearboxes, they fail too, and a 5 speed gearbox + a clutch rebuild is about the same as the auto. Hope it helps, as I believe that for the 9000CS, the autobox works more in harmony with the engine. (On the other hand, the Aero works better with the 5 speed).