There wasn't really any clear legal status to them; the unit of the USSR military that was responsible for them wound up in the Ukranian armed forces after the split, as did quite a bit of other material. Thus, the agreement.

They could have, at the very least, used them as raw disasembled nuclear material for their own program, if they had wanted. As the recording industry discovered, once your stuff is in someone else's physical posession, it's hard to stop them from figuring out how it works.