A couple things. First, the water pump does not create the pressure in the cooling system. Heat does it, and the pressure is held by the radiator cap. Ideally, the cap should vent air when the pressure rises above whatever the cap is rated at. When the coolant cools off, the cap should then allow air to enter the cooling system and thus avoid a vacuum. A failed pressure cap could account for the small loss of coolant.

Second, if the water pump bearings were bad, you'd hear it through the stethoscope. Listen to other bearings under the hood and compare what you hear.

Pressure test the cap when you pressure test the rest of the system.

__________________
1989 300 SEL that mostly works, but needs TLC