Chris, the notching and boring allowances would not apply to a truss, but would be at least a guide line as a starting place. If it exceeds the allowance for a joist, then I would tend to report it since the truss is more dependent on the integrity of all of the individual components, not as much "fudge factor" as the span and notching tables. Another reason for using this as a guide, is the picture does not show what your found when you probed. Just the fact that more than 1/3 is missing or not would be another way to look at it.
All things considered, the older the construction the more weight I would give to the functional success or failure. But that is just my way of looking at it, your mileage may vary
