The new weekly update is here showing the current amount of nuclear weapons owned in Metal Gear Solid V: The Phantom Pain. The red part of the graphs shows the changes since the last update provided (June 6th).
The current numbers, as of June 9th, are as follows:
Xbox One: 121
Xbox 360: 287
Since last update:
Number of nukes went up
Number of nukes went down
As you can see there was a slight increase on PlayStation 4, but all of the other platforms saw a decrease, with quite a dramatic change on Steam and Xbox One, as is evident from the graphs. This may have something to do with the anti-cheat measures Konami has introduced on June 6th – though, unfortunately, the company did not specify what these measures are exactly, and if they also affect unfairly obtained nukes that already existed.
Source: Metal Gear Official Japanese Twitter (1,2)