I never applied the armor maneuver penalties to weapon skills; I was under the impression that the penalties were just to moving maneuvers. Character Law (red band), p. 46, section 3.4, 'Maneuvering in Armor Skills', says that the armor penalty 'modifies Moving Maneuver rolls attempted while wearing that armor type.' So it seems to apply only to moving maneuvers.
Encumbrance penalties (i.e. dead weight), on the other hand, we applied to everything. But I can't see that spelled out explicitly in Character Law or Arms Law.