You need to get replacement air to the cavern when you pump the water up, and let the air to make room for the water when it's going down. So you need a separat

You need to get replacement air to the cavern when you pump the water up, and let the air to make room for the water when it's going down. So you need a separate shaft for airflow anyway. I assume the rest is just economics, it's probably a lot cheaper to have all the moving parts easily accessible on the surface. Edit: Also the fact, that if the pump was at the very bottom and it failed, you'd need to have an alternative way to clear the cavern of water in order to go down and fix the pump.