Tarm: Well that didn't seem to work. No auto missiles or torpedoes turret targeting. That sucks royally. Annoying buggers they are...
Unless you are going to invest in the Ordnance Targeting subsystem, and dedicate a precious sub system slot to it, and spend time away from steering your ship to try to snipe missiles personally (hmm...my prejudices about this course of action may be leaking through here...), the best process for shooting down 'torpedoes' seems to be...
1) Flak Secondaries, held down continuously during combat (added benefit of occasionally damaging/killing a fighter), and...
2) Either Tachyon cannon, firing A LOT in the general direction of closely approaching torps/missiles, or Proton cannon, firing when fully charged w/ the torp in the center of the yellow band.
Neutron Beams will actually kill a lot of missiles before they reach your shields, and may be the most effective torp/missile killer system for practical, operational purposes (other than the continuous flack secondaries). However, their kills don't seem to get
counted very often if you are trying to rack numbers for the Achievement, especially at the higher Mark levels. Honestly, I am toting Mk 6 Neutrons and Flak secondaries for many hours now, I typically kill at least 1/3 of incoming heavy missiles and torps, and I think that my count for achievement purposes has only incremented twice since I put in the Mk 6 gear. I'm switching back to projectile b/s for awhile to try to rack some more achievement numbers before I finish the game again.
There is a post buried over on the Steam forums somewhere in which Travis Baldree explains a bit about the "Torpedo Killer" Achievement. Short version: originally it was just torpedoes, but in reality now in the release version it is any of the heavier, slower, straighter missiles that get counted.
Except that my practical experience of a couple hundred hours in the game indicates that the counting of non-torp heavy missiles toward the Achievement, and even the counting of clearly blown away torpedoes can be very unreliable, especially as your technology level rises. I got credit for killed missiles just fine up to about 200 missiles intercepted / Mk 4 level gear. Since upgrading to Mk 5+ gear, over the course of MANY more total missions, I've only racked up 97 more torpedo/missile kills. (I'm hoping a change back to projectile broadsides may help with this.)
I can personally attest that small fast missiles, Swarmers, etc, that are easy for your flak cloud to kill, are NEVER counted into your "missiles shot down" number.
There is also a possibility, which I am going to test, that the game stops counting missile kills once you add on the Missile Deflection sub system. Or maybe just has a difficult time with it. That upgrade was about when my missile kill count slowed WAY down.