I'm guessing that the keg/scuba tank thing containing the uranium is bombproof, even for large values of bomb. So it's just a matter of digging them out again. Admittedly, if the underground spaces are completely collapsed that might be difficult. But I doubt that 300' of reinforced concrete is completely collapsed.
Regarding the ventilation ducts... I have visited a couple of WW2 era fortifications. The entrance tunnels were like a T, where you entered across the top of the T and then turned. The idea was that a blast would go to the far end of T crossbar and reflect back outside without (much?) going down around the corner to the actual facility. There were 2 or 3 of these T junctions on the way in. I expect that exactly the same WW2 engineering would apply to ventilation ducts in Iran. So shooting a bomb into a ventilation duct wouldn't get it into the facility itself, just to the far end of the T, although that would certainly be closer than at the surface. How much closer? Who knows? It could be halfway or 3/4, but equally it could be 3ft.
So imho "obliterated" without knowing the engineering of the duct is just wishful thinking.