As I have stated before nothing is foolproof, BUT In my experience, when you have conductor insulation damage (BARE SPOT/blow out) from a lightning strike you have carbon from the explosion/short/arcing/flash over. I assume the aforementioned BARE SPOT most likely occurs at a weak spot in the insulation and the short is from the neutral or hot conductor to equipment ground conductor. At this point there will be carbon, I have never seen a bare spot/blow out that was not accompanied by this carbon, meg that you get a low megger reading.
Not condoning this, BUT assume you pull Romex/NM nick the wire and not notice it. You meg all the branch circuits and they all meg full scale of the megger you are using at 1000 VDC, you/I feel fat dumb and happy we did a good job. Ahhh but there is a bare hot conductor buried in the wall, is this safe? Not a good idea, not something I want, but what is this bare spot going to do in the next year, 5 years, 10 years..... This goes for the bare spot in the conduit also IMO.....
In addition to all this experience, common sense and your companies liability play into making any calls on lightning jobs or heck for that matter any jobs.