I think the Sterilization Hubs bug out when you planet crack them, as I did this in my game and it doesn't count as destroying it.
Here is what it looks like:
I destroyed all the other Sterilization Hubs normally, by just bombarding them with my fleets.
Here is what it looks like:
I destroyed all the other Sterilization Hubs normally, by just bombarding them with my fleets.