As far as I can tell the Mk. III Nuke is only for getting that one achievement for nuking every planet, then winning the game. Never considered using it otherwise.
It's a linear increase, I think, it hasn't doubled in aggressiveness since start, just added 11 extra points. If you went from 500 to 511 it would probably be the same change, unless i'm wrong.
Tractor beam: I think it says in the tooltip "Tractor beam x25 or whatever". I know, for instance, that the spirecraft martyr, which has tractors, labels the number of beams. I haven't checked the turret versions.
Additionally, tractored ships do not hit minefields, so the two should not be combined in a defensive setup unless more ships than are tractorable wind up coming through.