It would depend on the size of the lag bolt. Consider that on angled roof trusses (as in the trusses forming each side of an A) the underside of the truss is under tension, while the outer (top) side is under compression. So (using your notch example) a notch on the underside is much more damaging than one on the top. A lag bolt would similarly decrease load capacity but to a lesser degree than the notch. However drilling into the side of the truss (somewhere near the center) has relatively little effect.
