Last year I replaced the nitrogen cells on my 1987 16v in hopes of bringing life back to my shocks. This didn't do anything probably because the rear shocks are leaking. If I were to buy new shocks and put them on the car, would the nitrogen cells I just installed still work or did they go bad because I installed them with leaking shocks?

Running with dead accumulators can take a toll.

The fact that the shocks leak is not a sufficient reason for the system not to work. I suspect that you have a level valve or pump problem. But, sitting on the car at reduced pressures (or none)won't hurt the accumulators any more than sitting on a shelf.