I tried a bit around in godmode and I dont know if it is a bug or not.

I found out, that the glowing crystals dont give gems and that one cave gives only 1 gem. (It was a non glowing crystal rock) Is this a bug?

And did someone play this a bit longer? The caves aren't very small, so I dont know how it will affect the UPS if you explore 10 caves. Factosissimo2 does impact UPS and these are smaller.

For UPS, I don't know. Space Exploration can generate many big surfaces for planets, so the amount of surfaces is not a problem for UPS. But my elevator script that checks for power to enable the elevator may be bad for UPS.
The UPS impact with Factosissimo2 would be the validation every few ticks to teleport items in and out of the building. My mod use the same logic, so it may be a problem, but I didn't tested this much.

Crytals are decorative, they give nothing.
What you found is a gem crystal, there are 2 per caves, and they drop a gem. Each cave have a random 2 gem out of the 4 types, and the location is random (out of a list of locations the gem crystals can have)

Someone made a map ans spent a few dozains of hours in it (and explored caves) and had no UPS problems.