Now, it's common belief that by the time of FTL, nuclear weapons are outdated. However, that might not be the case. From pixel measurements someone else did, of the human compared to the Rebel Flagship, I remember that the flagship would be about 130 m wide, or something along those lines. A modern nuclear explosion of 1 megaton can cover 100 square miles, way larger than the rebel flagship. Any person within a six square mile radius would be vaporized. Also note that crew suits would not help, as in game, fire still damages crew, so they aren't immune to heat. This means that even if it didn't destroy the ship, it would at least do large damage and kill most if not all crew on board. Also remember that shields would not block any of the damage, as missiles in the game go through shields. However, there may be other reasons why you don't encounter them in game.
1. War Laws - It's unlikely, but there may still be laws that ban the use of nuclear weapons, despite the time of chaos.
2. No longer produced - As the time of FTL consists of large numbers of pirates, there could be a threat of a pirate getting access to this kind of weapon, which would probably lead to hard times.
Anyway, if you disagree with me, go yell about it in the comments. But whatever,
