The hole never disappears; at the end of the story, the first things that went into the hole come out of the sky and back into the city. There's no sign that the hole is gone.
The hole is first discovered after a typhoon. When someone shouts into it and then someone throws a pebble, they never hear the pebble hit the ground. Ultimately, nothing thrown into the hole fills it. When someone offers to fill it in, the mayor agrees. The man gets contracts to dump things like nuclear waste and government secrets into the hole. Everyone throws their trash—dangerous and otherwise—into the hole, thinking it'll be gone for good. No one knows how deep the hole is or how it gets rid of what's thrown into it.
However, one day a construction worker hears the first words shouted into the hole come from the sky. Then a pebble falls to the earth, though the man doesn't notice it. There is no indication that the hole itself is gone. However, the story implies that everything thrown into the hole will come back out, and the now-clean place will be more damaged than ever before.