I more like the idea of something extra to manage. I never really said I wanted crystal to be strictly finite in a case like this. If that were the case, well, it would suck for one crowd and be awesome for another or whatever. That kind of idea is too divisive and doesn't work with expendable things. If the AI invents a way to steal or destroy your research permanently, we'll talk the ability to use a strictly finite resource for the purposes of something that can be lost.
Also, I was totally thinking with the SC1 mindset more than anything else. In that game, you still get 1 gas from depleted geysers per harvest. It's a significantly lower rate and it's inefficient but you never really run out. IIRC, Keith mentioned something like your homeplanet or home command always giving you some sort of crystal supply. So, in that case you can spend time to get crystal. However, that goes back to the problem I have with building up stuff anyway. All it really does is take time. However, if you somehow lost crystal production or really wanted more, then that could well force you to actually go take more planets than you otherwise would-- well, not force, but encourage. You take that AIP hit, you get more income, you can possibly topple the AI homeworld. Or, if you ever get into a situation where you're totally screwed, you can always blow away the ships with electric warheads or otherwise and hope you can win before the extra AIP gobbles you up. I don't really like warheads myself, but if you lost tech or lost critical resources or made bad decisions at a high level, you take that hit to get back into the game. That's my understanding, at least.
I still support the idea of something different to what crystal is right now, regardless. There could be crystal asteroids on enemy planets. You take the planet, you get more access to the neutral structures that those are. They function a lot like the spirecraft asteroids, except that a mining vessel can build an outpost on them that soaks in the income until it dies. Works like a harvester. If it dies, the asteroid becomes smaller or is just gone entirely. Smaller asteroids get smaller outposts which gets lower income. What this allows most importantly of all would be crystal raids. Set up a beachhead for some extra cash. If you lose all the safe asteroids, you have to get more risky. It's a little bit like if you waste knowledge or just plain can't get enough, you take the risk of knowledge hacking.
So, instead of strictly limiting nodes, or permanantly lost crystal manufactorum sorts of things, you just take little hits to your economy if some sweeping force wipes out your crystal mining colony. Even then, you weigh the risks and benefits and only build what you need. The asteroids that you leave neutral don't take any damage at all from said sweeping force.