It wasn't just Superman who was scaled back - so was The Flash. Before the Crisis Barry Allen could run at multi lightspeed, after it he was retroactively scaled back to just the speed of light as a maximum. There seemed to be a change in the DCU physics where Newton's rules of physics were applied and suddenly no one could exceed the speed of light (bar the Pocket Universe Superboy and Mon-el apparently!).
Perhaps the so-called Speed Force is the retroactive explanation. If that's something that didn't exist before the Crisis, and was created by Barry Allen's death, it might have (whether purposefully or accidentally) created a barrier. As I recall when Wally finally learned to exceed lightspeed in the 90s that was when he first crossed the barrier that Max Mercury had dubbed the Speed Force.