Canberra was alongside in what are declared Naval waters. That means that innocent passage, on the water or in the air, is usually permitted but that they may be closed, and access denied, at short notice. Landing a drone on a ship is not “innocent passage”; so legally the Navy could take an appropriate and proportionate response to cause the operator to cease and desist. That has, in the past, included disabling craft breaching a closure when it has been safe to do so. This would include incapacitating a drone when there is little or no probability of injury to person or property. That would have been the case here.
However, the ship is alongside in its home port; and it looks to be at a time which is not normal working hours. So the probability of any of the Ship’s Company being on the flight deck, and actually seeing the thing is low. In any case, in home port, force protection at normal alert states is provided by the Naval Police who man the Dockyard, not by the ship itself.