The lithium chemistry has longer shelf-life, higher power density, and better performance in the cold. And they are lighter (which matters for EDC, in headlamps, in torches which float etc).

You can get lithium batteries in an AA form-factor, so I'm guessing you are bothered about CR123s. Whether they will be easily available in shops during a disaster depends partly on where you are. Around here my local supermarket stocks them as camera batteries. My understanding is that then there's a crisis, all the AAs etc are in high demand by everyone, and get sold out quickly, but people are less bothered about cameras and so 123s remain available.

One of the benefits of the long shelf-life is that it's more practical to stock-pile them at home. Then you are not so dependant on shops. If you have a dimmable LED torch, eg an SF L1, and you buy batteries off the internet, $22 will buy you about 20 batteries which should last about 800 hours of continuous on. That's a lot more than 3-5 days.

If you want longer than that, then I have to wonder what kind of disaster you are talking about - maybe this should be in the "long-term survival" section. I would be looking at rechargable batteries and a solar panel or petrol-powered generator or something. And then the chemistry would be Lithium-Ion.

I'm not telling you to use lithium, I'm just saying it's a defensible choice depending on the situation.