I'm pretty sure the defender gets a bonus die at long range regardless of whether they are shot at with primary or secondary weapons.
No, that only applies when firing primary weapons.
Do special attacks follow the same +1 attack die at range 1 and +1 defense die at range 3?
Secondary weapons do not get Range Bonus Penalties.
Does an ion cannon at range 1 get 4 dice?
Do missiles and torpedos give the target an extra defense die at range 3?