What can be hacked on the target vessel? For example, will we be able to disable or active self-destruct, open and close airlocks, and manipulate thrusters?

The Legionnaire's systems are dedicated to the specific and directed task of overriding and overcoming the docking/air-traffic control systems of the target ship, which in-universe is a sufficient challenge by itself. They are not able to address the other command systems of the target ship.