I seem to remember a passage in the Book of Atrus that mentioned steam power generators working off of geothermal vents that used to run the D'ni industries. I don't know how accurate that memory is though, or if it's even canonical, since not everything in those books is canonical. But that seems plausible.

I went to check the DRC forums, because in the DRC Discussions board they talk sometimes about D'ni technology and the equipment they were using and such, but I couldn't find any specifics on what they were using for power. They do say this though:

"After a bit of hair-pulling, I've finally got the doors to the gallery powered again. The power to the doors had been completely severed. It was obvious that it had been that way for quite some time, rather than just the usual gradual degredation from neglect we're accustomed to seeing."

So it sounds like there's some sort of transfer system for powering buildings throughout Ae'gura.

Anyway, it's probably that the D'ni had multiple ways of generating power, no? After all, we on the surface have a plethora of different methods for generating electricity, why would the D'ni be limited to just one kind in the cavern?