I'm also of the view that the anti-fighter trait should be reworded as ignoring dodge and stealth, with hits causing one point of damage. This neatly sidesteps the complaints that allowing shields to be useful would create exceptions. Even if it didn't, exceptions aren't necessarily something evil to be avoided, providing that they're kept to a reasonable level. For an example, see the Psi Corps and their Psychic Crew rule.
If you also wanted shields to work whilst intercepting fire, you could make the same simple change to the wording, and have the fighters suffer a point of damage whenever an interceptor dice comes up as a 1.
Overall with the above two rules, I think the big problem was the assumption that one point of damage will kill any fighter flight, which just isn't true when dealing with Shadow fighters.
On the dogfight front though, I'm sticking with the idea that dogfights should be much more decisive in nature, so the being completely destroyed if you lose is more appropriate. For this situation, the shields should be taken into account in the same way as the hull, weapons, dodge and stealth, which is to say that you don't worry about them individually, but they all are taken into account by the dogfight score.