In fairness to the inspector, he can only inspect what he can see. If there was no access to the attic, or if the attic was finished, there is no way he could see the holes in the sheathing underneath the shingles. He MIGHT have been able to tell if there was one or two layers of shingles on the roof, but frankly the only way to find these holes is to remove the shingles, or to see them from below. If you couldn't see them, neither could he.
If he had walked the roof and noted spongy spots, that's a clue, as is any evidence of leaks - water spots in your ceilings. Any of those conditions would be a red flag.