JIT isn't the problem in your last example, it's a weak supply chain. If you have a singular source for some critical or necessary thing, you have a risk whether you're using JIT concepts or not. Though higher if you take JIT to an extreme. Your sources need to be that, sources, and ideally geographically separated. See the various industry crises following natural disasters in Taiwan for why.
The proper, though not easy, thing to do is have some primary sources of your materials and secondary sources to handle surges and supply issues with your primes. You may still have a production slowdown, but hopefully not a shutdown. And like with backup, if you don't use them you don't have them. You have to place orders with all sources, and use materials from all sources to ensure that they are in fact up to snuff. It'd suck to buy your RAM from Foo until a flood, and then find that BAR's RAM doesn't actually work (or doesn't work with your motherboards).
But, having a single source is more efficient than multiple sources---you can integrate tighter with their ordering system, packaging, product quirks. Until it stops working.
Having all of your sources in one country is more efficient. Until it doesn't work.
Managing all of your materials just-in-time is more efficient. Until a backhoe hits the gas main in the street outside and you can no longer get trucks into your factory and have to shut down the line for the duration.
A company with a weak (but not completely idiotic) supply chain will have a significant margin over a company paying extra for a strong supply chain. Until something goes wrong.
I guess my point is that, in everything I've read and experienced, JIT isn't about efficiency to an extreme (drop to 1 supplier, have 1 uberefficient factory, have 1 expert). You still maintain a buffer, and if possible multiple suppliers. The source of JIT (in manufacturing) is primarily Lean or the Toyota Production System. Those do not endorse zero-buffers or sole-sourcing for the purposes of efficiency. The purpose of reducing buffers is to expose inefficiencies elsewhere. And you find the right level of buffering for you based on your suppliers and risk tolerance.
You do not have to live for ever, so surviving a extinction level ecvent is more than the "right" level.
Being so brittle that the failure of one delivery kills you is less than the "right" level.
How long do you want to live? And when you die, how is it going to happen?
It is pleasing to see firms go out of business in a orderly fashion, such that they have the resources to shut up the shop properly, and every one in the business gets "onto the life-rafts". But it is more common to see businesses go down in a screaming heap with huge debts and big messes for others to clean up.
When I was at business school I was taught that a firm should have the correct amount of debt such that it maximised the tax shield of interest payments and had no fat that a hostile acquirer could use to do a hostile takeover.
That was in 2007. I am quite sure the course teaches something different now!
The proper, though not easy, thing to do is have some primary sources of your materials and secondary sources to handle surges and supply issues with your primes. You may still have a production slowdown, but hopefully not a shutdown. And like with backup, if you don't use them you don't have them. You have to place orders with all sources, and use materials from all sources to ensure that they are in fact up to snuff. It'd suck to buy your RAM from Foo until a flood, and then find that BAR's RAM doesn't actually work (or doesn't work with your motherboards).