I've played a half dozen games and never once found a dust. I just spend my two starting dust and then can never upgrade the crystal again, and dark rooms are just ... basically empty because I can never light them.

Is there some trick to getting dust that I haven't discovered? Or is it just really really rare?

Yep, during your game you may encounter some Crystal Shard. 

Be aware that when you comand the Crystal bot to extract the Crystal Dust it will trigger like an "inifinite wave" same as when you go to the final door. Once the bot finished, it will follow you, so I will recomend you to go to the next crystal slot, or going into the previous position.

yeah they can be quite rare

Thanks for the explanation.

They seem much too rare and difficult to extract compared to the potential uses for it.

If you could earn an average of 1 or 2 dust per level, that would make for some interesting trade-offs regarding whether to upgrade a crystal or light a room. But it seems like it's significantly rarer than that, which means practically you're never going to spend dust to light a room. It's far too valuable to be used on something so unimportant. You're just going to occasionally upgrade the crystal.

Which makes the whole dark room mechanic pointless.

IMO it would seem easier to balance if dust numbers (earning and cost) went up by a factor of 10. Then you could find 5 here and 7 there, lighting a room might cost 3 dust while upgrading the crystal might cost 10 with an increasing cost each time.

Update: I found one dust node in my travels!

Suggestion: The crystal should definitely go back to its slot after harvesting dust, unless ordered otherwise. It started a huge wave and I battled and battled and waited for it to finish but it didn't, and then I realized the crystal was just walking around right in the middle of battle! (Ordered to follow the player by default after harvesting.) GET BACK IN YOUR HOLE DUDE.