i had a 93 90CS coupe that was a blast. I modified it, did alot of the work myself and with my buddies.
i didnt really have the car long enough for it to develop any problems, but i dont think it even would have.
In 95 they had the 2.8 in the 90cs which is a great engine, and because its based on the current VW (well... not current for much longer) V6, there are readily available parts for it.
You mentioned also looking into a 1996 A4, which might be a better bet. The A4 will give you a more modern look, with more of the amenities you'd find in a new audi. There are several for sale on ebay
for under $9,000 which would be fun. You're looking at probably the same engine/performance of the CS with a modern look and a cleaner interior.
The choice is obviously yours, you'd probably pay a bit more for the A4, but you'd get more for your money in my opinion.
If you're really concerned about the 90CS, look here
for recall information. Make sure the car you're buying has all these items taken care of PRIOR to the sale if you dont want a mess on your hands.
Good luck, keep us posted