While a small amount of whale hunting does exist, it's a fraction of what it once was.
Today, yes, mercifully, which is why humpbacks are no longer endangered. But the point is that the decline didn't begin until after The Voyage Home
came out. They were severely endangered in 1986, and it's only in the past quarter-century or so that their population has recovered.
We can assume, I suppose, that in the Trek universe, the moratorium on whaling did not go into effect in 1986 -- or perhaps it did for a few years but was then abandoned during the Eugenics Wars. Thus, in that reality, the humpbacks were not saved from extinction.
The problem with "repopulating" earth's oceans with George and gracies offspring would be the size of the gene pool.
Which is where genetic engineering comes in. The novelization covered that.