In today’s world, even though each nation is politically independent, they all rely to some degree on other nations for trade or security, or both. No nation -- at least no nation of even minimal significance -- exists free from this interdependence. But molecular manufacturing has the potential to change all that, and not for the better.
When individual countries are able to provide all their own goods and services, and no longer have need for import or export trade, they will have less incentive to maintain good relations with others. When economic security is no longer an issue, the only remaining security concern will be military.
Now we have all the makings of a terrible new arms race. Every country possessing unrestricted molecular manufacturing capability will have the ability to design, test, and stockpile massive amounts of small, cheap, frighteningly powerful weapons. Assuming nanotechnology development is allowed to proliferate, we can expect that many countries will achieve economic independence and unprecedented military prowess.
Will we then see a stable equilibrium, a tenuous balance of power similar to the "mutually assured destruction" of the Cold War? Not likely. Nuclear weapons require massive research effort and industrial development, which can be tracked far more easily than nanotech weapons development. Molecular manufacturing will enable nanotech weapons to be developed much more rapidly due to faster, cheaper prototyping. It will be nearly impossible to know with any certainty how much war-making capability your enemy, or your neighbor, possesses.
Less response time to an attack, and better-targeted destruction of the enemy's resources during an attack, will make these new arms races highly unstable. Unless nanotechnology is tightly controlled, the number of nanotech-possessing nations in the world could be much higher than the number of nuclear nations, increasing the chance of a regional conflict blowing up. Greater uncertainty of the capabilities of the adversary could promote caution -- but could also increase the temptation for preemptive strikes to prevent proliferation.
Worse still, this opens the door for the development of rival groups within countries. We might see repeated military coups, devastating civil wars, and dissolution of nations into large numbers of hostile, unpredictable, immensely powerful tribes. Another concern is that radical transnational groups bound by religious, cultural, or ideological extremism might make use of molecular manufacturing toward terrorist ends.