I had a new roof installed also after a hail storm. Three to four weeks later, I saw what appeared to be bubbles or peaks and valleys on my roof.
Not knowing much about roofing and my own visual inspection of my roof decking, which was ok, I called my roofer.
He said that the tar paper had buckled and that that is normal. The first hot weather we have the tar paper will adhere or shrink down and lay flat. Sure enough it did and I have a flat roof.
BUT, your comment about seeing light through the joints of the roof decking is another problem.
I do not understand that at all. Did he put down tar paper? The joints between the roof decking is not supposed to be sealed up. The first layer of defence on a roof is the tar paper then the shingles are installed over that.
Your light in the decking is something that another expert will have to address. Are you sure that you are seeing light between the decking? If you actually are, then you will also have a river of water. Has it rained since your new roof?