Thats because the beam itself doesn't give off any light. Its the point of origin and the point where the beam hits that give off the light.
Couple of ways to test this: Create a situation where the beam passes near a ship without hitting it and see if the beam lights it up. And fire the beam off from a turret that isn't close to the hull. Like a multipart turrets on Orion. That way the point of origin is away from the hull, and should light up the hull (assuming the barrel isn't in the way), unlike the deimos where the beam is fired from a singlepart turret.
(Note that I have not tested it, and are unable to test it now 'coz I don't have FS installed. I'm just making conclusions)
Same thing with the warp lightning. Theres one point that gives off light. And that point is inside the incoming/outging ship.
I could draw it, but you're so smart that I don't have to.