It depends on how managable the risk is. For a level like the Eden Starship colony game, I always go for the ore that's covered by lava, but that's only putting the mine and trucks at risk, and you don't usually lose the trucks if you're paying attention. The only real risk is if you somehow don't expand to another mine before the first is destroyed and you run out of money. That's not too hard to avoid. For the plymouth starship II level, I usually go for the ore covered by lava, but I don't build more than the mine and refineries on ground that gets covered by lava.
The cost in both ore and time of replacing an entire base is pretty big. If it's an area that would put my whole base at risk, then I'd probably avoid it, and if I needed the ore, I'd just tube to it. If you have no money for tubing early game, then I'd probably put the smelter far away with the rest of the base, and use the first few truck fulls for the tubing and a new smelter.
Earthquake zones seem like a bad idea. They do too much damage to vehicles, unless they're far enough away from the epicenter, and the quakes aren't very large. Hiding them in a garage takes a lot of time, and if the building goes, so do all the vehicles. I have to question if mining a higher yield only part of the time, versus mining a lower yield full time is really worth it. In terms of raw ore rate, it probably is, but if you consider the max storage, and how trucks will stop when it's full, then maybe you're getting less utilization from the higher yield mine then you think. The down time can also be pretty bad if there is fighting going on, and you need to be constantly producing vehicles. That ore can dry up pretty quick if you're not harvesting, and having a zero production rate is not good. Plus the time it takes for the extra management of the trucks will slow you down. Or from the other end, if you're busy with something else, such as a battle, you might forget to take the trucks back out and resume harvesting. I'd say if the quakes are strong enough to warrant making your trucks run and hide just to survive, then it's a bad idea. They should at the very least be able to survive the quake if left on their own, and maybe just require the occasional repairs or replacement.
Hmm, actually, why do earthquakes even hurt vehicles? Doesn't it seem like they should do much more damage to structures, and almost nothing to vehicles? (Unless a building fell over onto them).
Btw, I don't think proximity to DIRTs helps at all. I'm pretty sure it's more of a global thing. (Although I'd have to check each possible type of damage to really be sure, but from what I've seen so far, it all appears to be a global percentage value).
Oh, and here's a thought. Let's say you pull off some risky gamble and get more ore, that may help increase the chance of your survival, but if you're constantly choosing locations where you can stand a big loss that will mean the end of your colony with some small probability (fixed or at least bounded away from 0 by a constant), then in the long run your colony will go extinct with probability 1. (This sort of ignores evacuating the planet to safety, and hence having no real long run). Anyways, just a thought for you risk takers.
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