Probably the two biggest money eaters on old S2000's are the roof and the geo bushes.
The roof is expensive to replace/fix, so always check for wear marks on the side where the roof mechanics hinge, this is the common area for wear and holes to develop.
The bushes are famous for seizing. Which can result in very expensive labour bills to repair. Once these seize any sort of geometry work is impossible, so ask questions about when it was last checked and greased. It's not age related either. You could have a '99 car and the bushes will move or a '07 car and all eight are solid.
If you do take a punt on a older cheaper car that has no history of the bushes being looked at get it booked in with someone that know what they are doing, preferably a Honda specialist as they will be well prepared for what may be likely. Once checked, get some new bushes in there (OEM are fine) and plenty of grease and you will be a happy chappy.