im pretty sure that it increases both phy and mag damage... if you unequip a weapon then reequip it you get more phy damage and mag damage than t he weapon says you should get...
kyrillos
4X
fire shield spinner
DarkRegime
Avalon alliance
although you don't attack with the weapon, i still think the weapon affects your magical nuke damages or else people could be using level 1 weapons?
i not sure if the masteries increase nuke damage...but weapon masteries are not force masteries so i would assume that weapon masteries and force masteries DO NOT stack.
that's also the reason why some builds forsake all of the weapon masteries and concentrate soley on nukes