sometimes I see wavy roofs after completion and before a hot summer. Somethimes this wave is only the tar paper being wavy and not laying down properly yet.
I know after our last hail storm, our roof needed re done, we did a two layer strip and down to decking.
They layed the tar paper and set down comp shingles. Two months ago I noticed that waves and what looked like raised areas. I called out the agent and he told me this same thing. Sure enough after our hot summers, the roof laid down nice and smooth.
Now, the decking should always have the clips. But if not there, not much to be done, or I dont think you would want the roof removed just to add clips. Tough decision.