The cruise missiles in question were not inside the aircraft, they were attached to the wings:
Warning, some Army speak here but the principle is the same. The Dept of Energy makes a physics package, the warhead, to specifications of the requesting service or services. Size, weight, yields, other factors are included. The service then builds an “adaption kit - Army parlance” to adapt the warhead to the delivery vehicle. It could be an artillery shell, missile, rocket, bomb, etc… The adaption kit contains much of the fuzing/sensors/timing/initiation chains to interface with the warhead. Also, physical attachment points for the warhead and attachments to the delivery vehicle. And the skin section for aerodynamics, sex appeal, whatever. Army speak again; warhead+adaption kit= warhead section. The adaption kit can be installed on the delivery system without the warhead inside or have a conventional (high explosive, etc…) warhead installed and show no physical difference. Multiple systems could use the same physics package, an example would have been the Nike Hercules missile and the Honest John rocket. Same warhead, different employment.
As others have said; there is a chain of custody for the warhead. Everyone who was in the chain is in serious career-threatening trouble. You never “lose” a nuke.
Update: ‘70 punished in accidental nuclear flyover’
From the article cited by Johnny L.A.:
Heh. Here I was thinking "Typical service, they had said they were going to do a stand down over a month ago, now I read that they are just getting around to it NOW?
than I read the dates on the post