I'd be insterested in seeing photos.
One big reason for "wavy" or "humpy" shingles is having shingled over "buckled" or "rippled" felt.
Felt can be buckled or rippled from moisture in the felt itself, right off the shelf, or from rain or snow, etc. Even though the felt may appear totally dry, it can retain moisture, untill it's had a chance to dry out, depending on sun, hunidity, etc. Where I work it can dry out, and shrink perfectly flat in as little as an hour or two. In humid conditions, it might take several days. The felt buckling CAN be "worked out" fairly flat when shingling through the use of extra nailing. But once it's been installed that way: shingled over, it probably will stay that way for the life of the roof. I know of one job I saw guys doing, in the middle of actual snowfall, which still looks that way 10 years later.
There's a possibility that one MIGHT go back up there, and carefully lifting some of those shingles, install extra nails here and there to suck it back down, but they probably won't ever look like they could have if they were installed over a flat surface.
One who enjoys helping with roof problems, for the fun of it.