I wrote this is because while I was playing Humankind yesterday, my vassal attacked me, launched nukes to my capital city for I ask it to change its nuclear policy, I’m pissed, because I have conquered every city that owns Uranium to monopoly the nuclear weaponry before anyone could use it to threaten my homeland, now my vassal took an free ride in developing nuclear weapon and used it to bombing the first city I built? I’m speechless. 

This is the issue I also observed in Paradox game Victoria 3.   The subjugated empire seem to enjoy the fruits of their overlords' conquest and stab them in their back once they become strong enough. It is, with all due respect, ridiculous and unreal. 

The colonial empire does not “share” their resources with the nation they colonized.  The whole purpose of mercantile colonization is to exploit the resources and raw materials of subjugated nations while selling the product back to them for money. It is not an equal relation. Therefore, the overlord is not going to share their resources but exploit the resources of the empire they conquered.  On the other hand, although free trade is the predominant trading philosophy in the world, there is no country that would allow other nations, ally or not, to purchase every resource they have, especially things like uranium that allows nations to establish nuclear deterrence. 

May I suggest setting the status of subjection level to improve that situation of vassalage issue. For example: 

Puppet states: 

The states have no diplomatic independence but have most of their sovereignty preserved, overlord has ultimate military access and diplomatic sight over the puppet states.      However, the puppet states control their own religion (but limited only to their own territory), they don’t offer tribute money or influence point to their overlord.      Less resistance 

Dominion:

 Incomplete sovereignty, shared military access diplomatic sight, Religion controlled, influence point belongs to the overlords, offer percentage of their income to the overlord, free access only to luxurious goods overlords produced.   Considerable resistance form subjugated nation 

Colony: 

No sovereignty of any sort, completely subjugation, resource owned by overlord, the colony lose the control of the resource they produced, they have to purchase their own resource.   The overlords can produce the emblematic units of subjugated nation for free.      International outrage (serious diplomatic penalty) and strong resistance from subjugated nation.

 As for trade: 

Instead of saying trade every resource in luxury or strategic category, establish isolationism/Agrarianism (no trade at all), mercantilism/protectionism (states control), free trade (no restriction except uranium) let the player, AI decide which resource opens for trade which reserve for their own use, with that came new casus belli like trade war.