I think it's a huge stretch to link soil sample info to nuclear weapons, especially when uranium is such a common ballast material in military equipment. I think it actually just makes more sense that Israel is using uraniam counterweights in their bombs, and that's the source of this data.

I also think the article is underselling how straightforward it would be to detect atmospheric use of even very low yield nuclear weapons. There are many nations not aligned with Israel who do space based monitoring of that kind of stuff.

They would obviously use them if they could get away with it.