Actually, in the four instances where nukes have been actually used since the upswing of the mana cycle began, you've had:
Lone Eagle incident - Failed due to unknown causes
Libya - Worked like a charm
Cermak - Contained within a VERY powerful barrier
Crash 2.0 - Magically altered nukes didn't behave as they were supposed to.
In two of those cases, there wasn't any question about magic directly influencing the nukes. Cermak was literally buzzing with magical activity. In addition to the ward, there were all the people getting converted to bugs inside the building. In Crash 2.0, a bunch of crazies took some nukes, and started trying to magically enhance them. In both cases, there was magic directly in play trying to screw with the function of the bombs.
In the Lone Eagle incident, either no one knows why the bomb didn't go of, or no one is telling. It could be that there was magic affecting the outcome, either in general or consciously guided (remember, the immortal elves, at least, were active in the US back then, preparing for magic to come back all the way). It could also have been a dud. Yes, any machine has the possibility of a breakdown, sometimes even a catastrophic breakdown. It doesn't even have to be obsolete to break, either. Only restricting myself to the US space program, I'll give you three examples of SOTA tech that failed catastrophically because of minor problems no one caught: Apollo 1, Apollo 13, Challenger. All three craft were SOTA at the time. All three had major failures because of something minor. Apollo 1 had a pure oxygen atmosphere, and yards of velcro and other flammable materials in it. One spark, and it was a funeral pyre. Apollo 13 was critically damaged when a wire caused an arc in one of the oxygen tanks, which made it explode. And Challenger blew up because of a faulty valve smaller than a football.
Do you know why, at the height of the Cold War, the US had enough nukes to vaporize the USSR at least ten times over? Because they EXPECTED some of the rockets to fail or even be intercepted. You launch several missiles, so that you are sure that at least one will hit the target.
And actually, the Chicago hive was kicked over on August 22, 2055. The spin was a new wave of VITAS, yes. But on October 1, the Cermak blast happened. Nuclear detonations are quite distinctive, so there was no denying the blast. On January 21, 2056, the Bug City upload hit Shadowland, and was spread through the Shadow Matrix. From there, it spread to the public awareness, despite the UCAS government's attempts to silence it. There was some blowback against KE, but most of it was subsumed in the face of the fact that THERE WERE GIANT FRAGGING BUGS TRASHING CHICAGO! Kindof falls into the 'last resort' category, for most people. But someone using nukes for anything that wasn't so cataclysmic? Yes, there would be hell to pay.