What if, during the fighting, the Devil Fruits Tree was destroyed/burned down? Maybe the fighting was so fierce that it was destroyed, or maybe someone destroyed the tree specifically so that Rocks could not get his hands on it/use its power. The end result: the Devil Fruits fall into the sea, and then the chaotic currents of the One Piece World spread them all over. Eventually, the Devil Fruits wash up on random islands, or are fished out of the ocean by random ships, and are put to use.
This would explain why there aren’t many Devil Fruits in the Blues, to the extent that they are practically a myth. Because (assuming that God Valley is in the Grandline) the Devil Fruits wouldn’t be able to be pushed through the Calm Belt, an area void of currents. Most of the fruits would be located in the ocean around where God Valley once stood (the New World), some would drift even further down the line (Paradise), but barely any would make it all the way to the Blues.
This would also explain Wano’s lack of knowledge concerning Devil Fruits, and their shortage of them. The harsh currents surrounding the country wouldn’t allow many devil fruits to float to their shore. The main way that devil fruits would be able to enter their country is through outsiders like Kaido, but they are an isolated country.
So, the Government loses control over their superpower factory. And, now that pirates have access to the devil fruits too, the playing field is leveled enough that pirates are a legitimate threat. The Yonkos emerge, crews that if combined could actually rival the Government’s own power.
The World Government would still likely have several powerful devil fruits in their possession. I’d imagine that the powerful devil fruits that dominate the upper branches of the military are powers that have been passed down in their ranks for a while, for example (thinking about all those logias!!). In addition, they could have “harvested” the tree of new powers before Rocks attacked, meaning they still have a stockpile in their possession.
This could explain how the Government gave the devil fruits to Kaku and Kalifa in Water 7, but seemingly had no idea what powers it would grant them. They were part of the last harvest of the tree, saved for an important occasion.
But this stockpile is a limited source now, without the tree. It can’t last forever. And the Celestial Dragons are greedy and careless, giving devil fruits to their slaves, etc. This could be why they are so desperate for Vegapunk to create artificial devil fruits. They want to have the unlimited supply they once had, and to be able to produce new powers, instead of recycle old ones. This could also explain Kaido’s desire to perfect his SMILE devil fruits; he understands the power that control of devil fruits brings.