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Only a small ammount of fissionable material actually undergoes fission.
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So yeah, a lot of the stuff is just spread over a large area. Of course modern nuclear weapons are more efficient, but the Fallout universe is modeled after the late '40s-early '50s and the technology is supposedly, and weirdly, stuck in a state near of back then but still more modern... well, not that the Fallout Universe makes much sense anyway, but who needs realism if you can use a gatling laser gun to melt away hordes of super mutants.
edit: also, fission doesn't just make the stuff disappear, the uranium decays to other, also radioactive materials.
Fusion on the other hand doesn't have that problem so much and there are fusion bombs in Fallout ... but then again usually a small fission bomb is used to set off the fusion reaction, sooo ...