The surface on a water pump and where it attaches to the engine block are milled perfectly flat. When changing a water pump, the gasket that comes with the pump will seal perfectly without any silicone sealant.
Some mechanics routinely add a thin layer of silicone sealant to every gasket they install, including those on water pumps. It's a measure of insurance against the gasket leaking and a disgruntled customer.
Adding a thin layer of silicone sealant to a water pump gasket won't hurt anything but shouldn't be necessary to prevent the gasket from leaking.
