[Q]

You are right and I would even dare to call this a bug.
Why is it allowed to target a vehicle with a weapon that can do no damage at all to this vehicle??
In my opinion shield depleting weapons should only be able to target ships/bases, because what you describe with fighter is true for all units IIRC including weapon platforms.
Less dramatic but still a problem are shield skipping weapons like e.g. null space projectors, because they will do damage on units but their shield skipping effect is futile. The shields of the units are treated as normal hit points and not as shields.