Most of this is deliberate - I might not have explained it very well though.
The resources are still eliminated inside the crater, the main difference is that they are no longer eliminated in a large area around the crater (originally the entire fireball removed resources, which is a huge radius compared with the crater) I didn't realise that you meant the setting to prevent the nukes from destroying resources in the crater.
The new crater system is very different to the old one: The 'high' area around the crater is impassible, but can be mined like any other tile (e.g. concrete), and the inside area is like a hole (so needs land-filling) Craters-filling-with-water has no effect on the new crater system as a setting, as it only applies to the old system (I kind of forgot it existed in the new update) this is because the purpose of the setting is mostly to prevent problems the old system had with destroying buildings built on the crater, which the new system does not have (as you can landfill the crater in advance).
TL;DR: You should find the mod is now less aggressive in destroying resources around the crater, so less tip-toeing is needed (fire the nuke just outside of the resources). If you can't pass the new crater, try deconstructing it with drones, laying concrete over it, or mining it (with a tile in hand), then landfilling the middle.
Just generally, I am interested in what you think of the new crater system - I wasn't sure if it would be really cool, or kind of weird, so what do you think?
And on the original topic: is the 'crater only' approach to resources enough, or would a 'don't remove any resources' setting be better?
Thanks.