Aquifers aren't necessarily big underground lakes in a cavern. The water is often spread throughout the substrate kind of like a sponge. When you take the water out, it doesn't just leave empty space, the ground around it fills the void. To reopen and fill those voids would require pressure -which is costly.

There are things called recharge dams which sort of do this though. Problem here again though is cost. Usually other methods are cheaper which is why we don't see that kind of thing very much.