Against small targets like Vanduul fighters I expect you are just shooting at whatever you can hit. That's to be expected.
I think what you aim at on a larger target will change depending upon your intentions. If I were planning to take a Polaris intact through boarding, what I would target would be different if attacking through speed as it would when attacking through stealth.
If you were just chasing down a Polaris with a squadron of Vanguard, I think you would have to drop a shield quickly (means pack the S5 laser on the chin) and slip some Arresters through. That should kill every system on the ship except the manned turrets which would probably still work, and which then means you have to aim at some of those turrets to clear a path to board. The worst part of attacking a Polaris this way will be coping with their S3 missile capabilities. If you can shoot down incoming missiles with the Vanguard dorsal turret, makes life easier.
Once the shields and computer are down, the manned turrets are the real problem. You want to destroy as few of these as necessary, for you are damaging your future plunder, and there is no point in wasting valuable time hitting anything you don't need to. Probably need to remove 3 turrets to clear any approach to a Polaris. Forget the remote turrets--they won't work with the computers down.
Against a Polaris with a stealth attack, I am not even certain you need to worry about the shields. If you spike the target when you are within seconds of boarding, you should at the same time eliminate any manned turrets facing your boarding position of your craft (Prowler), which could be as few as a single turret. The guns on the Prowler will be sufficient for this. Depending upon just how effective Prowler stealth is, you could get away with almost no damage to the Polaris and none to your attacking craft. Stealth should be scarier, and really it seems to me it will be. Note though, you still need to spike the Polaris and the Prowler has no missiles, so you want at least one Eclipse. Given stealth is the powerful tool it is supposed to be, one Eclipse and two Prowlers should be more than enough to take down a Polaris, with almost no damage to any craft, and depending upon team effectiveness, you might do it with just one Prowler.