Just continue playing. Skyre-AI only have one nuke for the entire campaign. And only Skyre has that. Other rat-faction are annoying, but don't have such nukes.

If you play skyre yourself, you can build those nukes in his workshop (and are starting with one.) But the AI doesn't have the workshop as the player has. I think the workshop-units will get available for him at a certain point of the game, automatically, if even.

That said, I don't know, if there is a mod, which deactivate the nuke. But I think it just isn't necessary.