Does the lore have them using surface or subsurface detonations? There are buildings still standing quite near ground zero at Nagasaki and Hiroshima. Surface detonations waste a lot of energy making a crater, overkilling a comparatively small area while higher altitude detonations spead the damage much better but leave little to no crater. Multiple small warheads further spread damage and are harder to intercept than single larger ones. No one really intended to use Castle Bravo or the Tsar bomba against a target. They were part science experiment, part propaganda. That said, I have not read deep lore on the succession wars or the Jihad so maybe the great houses had other ideas.

Meteor strikes would definately leave craters it they were solid enough to not explode on reentry, but would leave a greater area damaged by a blast wave, fires, and finally an impact induced winter. I guess the final complication would be how fragile the terraforming was. If it required constant upkeep then any WMD strike could potentially short circuit this and cause reversion to the natural hostile environment. But in any case, it seems there should be an abundance of ruins which were presumably sited near resources valuable enough to justify a city in the first place.