Best practice to define bidirectional pin in top level design file with Quartus II?

The first warning occurs if you define a bidirectional pin, but don't use it bidirectionally.

The second warning occurs because you apparently did not define both pins in the pin planner.

Hint: A design that doesn't drive all output pins by actual logic or has unconnected input pins will always generate some warnings. You should write a useful and complete module definition, e.g. the model of a unidirectional or bidirectional tri-state driver.