To me it seems like nukes are a necessary threat. They only appear in meaningful numbers on the high difficulties, that is emperor, immortal, deity. They are the only means by which the AI can seriously prevent a player from winning in modern era if he or she played successfully until that point.
Without this, the game would be decided as soon as the player overcomes her starting disadvantage and pulls herself onto the development level of the AI. Of course the player can make a lot of mistakes and bad decisions and thus lose the parity, but generally speaking, if the player was good enough to reach an even footing in the first place, she is good enough to stay on that level or even push ahead.
My understanding is, that a single player game in modern era on the high difficulty levels has the player close to reaching his victory condition of choice or else, the player being close to be wiped out. Parity with the AI in this game is de facto a winning position.
This is why:
In games on these difficulty levels, I would assume that one has a good grip and understanding of the game and how to win it. The AI does not have such a thing as understanding and on top of that, many AIs are even programmed not to pursue a victory condition with full power. There is a number attached to each leader, that describes how consequently he or she works towards the victory condition of their choice.
For Alex, this number is high. For most AIs, it is not.
Consequently, the player has a large advantage. The better she understands the game mechanics, the more she can use them to make their victory happen. Everything up to and including immortal difficulty can be beaten by the player if she learns the mechanics and uses them. Even without the 'tricks' people might or might not consider fishy.
So, nukes are the only real challenge the game provides aside from overcoming the starting situation. If you take this out, the game becomes boring as soon as you reach parity.