Enemy ships which are being targeted by target painters and tractor beams should have priority to be shot at. Especially if both the weapon and the target painter are on the same ship.
You can make an anti fighter frigate with two anti fighter missiles and two tractor beams, but the missiles will often fire at a different target than the tractor beams. I very often see a fighter happily fly away again after being tractor-beamed without having been shot at. Same with target painters, ships which are target painted are very often not being shot at, not even by the ship that’s target painting him.