i do think the superweapon idea is right, with it being the source of corruption. Basically they set up the Cluster experiment and then went Scorched Earth with the surface
But I am pretty sure Yellow Diamond suspects the CGs may be alive. Or at least she has this middling hint of it.
Peridot likely reported seeing gems on the planet, so that's why YD sent Jasper with her: a veteran that could identify if any of the gems was Rose Quartz, the likely one to survive given the events that ended the war.
And when Peridot gave her report and said the ship was destroyed, you could just feel the tension when YD went "by who?"
Bitch may be in denial, but she knows there's a chance the CGs are still alive. Probably doesn't feel threatened at all though as she doesn't think they can stop the Cluster at this point.