If they had frozen genetic material/the means to clone why wouldn't the people of Earth future have already repopulated the oceans?
Its been ages since I read it, but I seem to recall Vonda McIntyre's TVH novelization addressed this issue. They did have the genetic material/means to clones whales. However, since no living humpback existed there would be no adults to raise the young clones. George & Gracie would become foster-parents to the new population of whales, raising them and teaching them.
I'm not sure that is a 100% solid explanation, but it made sense when I read it as a kid.
"Canon is only important to certain people because they have to cling to their knowledge of the minutiae. Open your mind! Be a Star Trek fan and open your mind and say, 'Where does Star Trek want to take me now'." - Leonard Nimoy