As I picture it, I think that there can be a minute leak that water can barely leak from. That leak could be to outside of the pipe, or it could be through a lower check valve, and a bit of water exits the pump. If there is no check valve in the way, the pressure tank will maintain pressure, so no vacuum forms.f I understand the check valve issue correctly, and I'm not pretending that I do, multiple check valves interfere with the normal, somewhat gentle pressure ramp up/down as the pump starts and stops. The water hammer is actually caused by the resulting, momentarily higher pressure wave.
If there is a check valve at the pressure tank, then that tiny leak will cause a vacuum to form. Then as the pump starts, the water column rises, gaining momentum, and slams into the check valve.