I mostly just ignore them. They die to my fleets main weapons incidentally as those ships travel. The AI can't concentrate enough fighter firepower to be a big threat to the kind of ships I use.
So I'm reviewing a video fighting against a remnant ordo with 2 Radiants and 20 fighter wings, with vanilla-only ships (I go over the vanilla DP cap, but only a little, I have max battle size set to 1000 but deploy only 325 out of 555). What I see happening is that all the enemy fighters cluster in between my fleet and the enemy on the first clash and die to a combination of Autopulse, Terminator Drones, and standing in the way of a Khopesh Bombing Run. 40 seconds into the fight I see only 13 surviving enemy fighters out of the original 20 wings of fighters (a few more reinforcements are on the way). After that, fighters aren't a problem for the rest of the fight.
Only Remnants rely heavily on shielded fighters in vanilla. Persian League uses enough fighters that I consider them a threat (more than remnants), but most of those aren't shielded.
Here's the video: