Why nuke cities when you can just bomb factories with precision? We already have technology capable of sending a missile to a specific seat of a car. US military has been deploying missiles that just have big swords on them now because they are precise enough where they don't have to bank on a large explosion to ensure they hit their mark. If the enemy opted to shift manufacturing into homes or hide it otherwise, you could just have an agent on the inside who marks these targets from the ground and they are later destroyed with precision.