Is this the waterpump you have M8501-D50:
There are only 3 ports that I am aware of.
One of them is for the lower radiator hose and the other two are for heater and thermostat bypass hose connections.
If there is an additional port into the waterpump's impeller chamber, you could just plug it. If you want to use if for an alternate heater port you could do that as well..