Runes that add damage types would take into account the size of the weapon, not whether the weapon already had the damage type on it. For instance if you made a platnite two handed polearm and added an energy rune you'd get a better bonus than if you took a platnite shortsword and added an energy rune. In this case it's the size of the weapon that matters rather than the weapon itself.
I think it should depend on type of rune (damage). I.e. impale, crush, etc. damages should depend on size (and type) of weapon, but electricity, signing, etc. should not.
