That's why the incredibly awkward idea of instituting yet another hull type. In summary, my (awkward new hull type) idea would be to give them a much diminished and more niche role, making them less useful overall. If you feel you're losing some regular damage potential on your chokepoints, shift the burden to (buffed?) lightning turrets.
Alternatively, a thought exercise, since I'm not that great at judging ranges once you get below three thousand. Would flak turrets be more effective if they were more like plasma siege starships? That is, instead of an area attack, you would damage X nearby units. As long as drones come out one by one, rather than like a hive golem, you'll have potential spacing issues unless the drones happen to be targeting something at your position. Would this allow more effective screening against passing elements than ships grouped around their targets? I've been much happier with Plasma area damage, but that might be due to a shiny effect and visible engine damage rather than anything objective.