It does sound like you have an air leak in the suction line and yes air can be drawn through clay soil. Air molecules are so small that they can be drawn through things that will not pass water, clay, or other substances. If you can move the pump to the cistern or install a submersible pump in the cistern, then this line will be a pressure line instead of suction line. If not then you will need to fix the leak in the underground line. You could lay a new line on top of the ground and see if the problem is fixed. If that fixes it, then you can bury the new line. Usually easier to bury a new line than to dig up the old line. Another idea would be to remove any check valve at the booster pump and install a check valve at the cistern. When the pump shuts off, this line becomes a pressurized line and either the leak will appear or the pressure in the tank will drop while no other water is being used. This might help you find the leak but, it will still need to be repaired.