Maybe they fly over it? Not sure.
I’m not leaping to the conclusion that it was a bomb, just saying that I wouldn’t neccessarily poo poo the idea.
Thunderstorms can go up to 40,000 ft, you don’t just “fly over it”.
Commercial airliners cannot overfly very large thunderstorms which reach above 60,000 feet. Some people do know about this stuff. You should just read, and not make uninformed speculation.
ML/NJ