There is actually some validity to this point. Interestingly, on ships that don't have targeting bones specified, the game will actually target its hardpoints. Take the Executor out against my jury-rigged MC80s that have only 8 firing bones and you'll see this. Specify a targeting bone and it'll aim for the center (or wherever you want to put it). I didn't notice this until after the release, so it turns out that you can aim at some ships better than others because of this. Oops.I think I did see some targeting bones on ships when looking.. I'm pretty sure there's something to that, as ships like the RSD don't seem to have many (generally every shot hits the center, or the bow). But I don't think you can rig it to do damage to weapons without actually enabling viewable hardpoints. I'm not sure though.
But by the same means, you ought to be able to make hardpoints destroyable without being targetable. I think. You just need to give them health values or they will come pre-destroyed.