One possible method of implementing scarcity into the game as a resource to be fought over would be to have that resource exist somewhere (on a certain sphere perhaps) for a limited time. This could prevent one alliance from effectively gaining and then maintaining control of the scarce resource for eternity. Now the length of time that the desired object exists for could be dynamic. You could possibly have it where there is X-time units of the resource available (similar to kWhs for instance), where if a few controlled the resource it would last longer, or if more controlled it then it'd last a shorter period of time.
e.g. 100kWh of energy available, say each person represents one kW, the if you have 100 people accessing the resource then it shall only last for one hour, however one person could access it for 100 hours.
Now obviously time units would be different (in days say), but if there was a team/colour event where membership was exclusive (top 100 per colour or something similar, or a different mechanic perhaps), and the event was significant enough to be fought over then that'd probably get some conflict happening. If there was even some way for alliances to raid a sphere to deny access to the bonus to other alliances then that'd have an effect on conflict, surely.
With a time limit for the bonus to be in play it'd also stop someone or some people from gaining control of the bonus for eternity.
Secret aid would be an interesting thing to implement, though I'd imagine it'd require a large change to the current spy/espionage system if spying is to still be an in game function/action. You'd need some way for the aid to be uncovered (odds of some sort to maintain some risk) which would be hard to do as the action wouldn't be directly attacking another nation so how do you determine spy odds? Also, if secret aid were to go into effect I'd enjoy it more if it were possible to send hardware such as nukes instead of just finances or a few soldiers.
Finally, nukes are still just large cruise missiles. If you want them to have a truly fearsome reputation (like they did way back when only the top 300 could buy them), then they need to do some sort of Percentage of Infra destruction. And if that happened you'd probably need to pare back the amount of nukes people can stockpile.