I'm with zhuliks on this, the necromancer's scrolls are pretty clear that there's some dark and evil soul-harvesting thaumaturgy at work in the golems. I suspect the crystals are just the vessels that hold the souls (or whatever is left of them) since a suit of armor did not have a soul to be conjured in the first place.
Some people have suggested the necromancer may not know or understand what he's talking about, but we're talking about a guy who (according to the scrolls you find everywhere) can raise the dead by basically just wishing it, read and control human minds, and even telepathically distract Sir, who is in all likelihood one of the demons sent forth by the Guardian of the Underworld (assuming the books you find on that subject are not complete horses**t). It's fair to assume he can recognize magic when he sees it, even if it is much more advanced than his own. That was actually his purpose down there, to research all those goodies hiding in the Underworld and return to Thaven. He's not just a necromancer, he's sort of a scientist too. In my journal I alternate references to him as "necromancer" and "researcher" quite often.
Anyhow, in the golem foundry you can see them made, looks pretty mundane, the crystals are pretty much the only weird thing about the workshops. There's a machine that I assumed to be an infusion chamber of some sort too, but I could be wrong about it's purpose. All the other workshops look like prettu regular smithies and foundries with the usual tools of the trade strewn about. I think the golems are regular (albeit oversized) armor suits, made from the weird metals found only in the underworld, possibly infused with some thaumaturgic energy, and powered by crystals who are themselves powered by evil soul-stealing/rending magic. There's a few ways to look at it in the end, but the evidence you find in game point to something close to this.
*edit* you'll also note the area has multiple arenas and some scrolls suggesting their purpose was not only to train in combat (in one note found in an office near the fighting pits, a guy says he's getting a lot more people come to him since people started getting killed but he's disappointed because they're not coming for the right reasons). I think the arena was for devout volunteers of the creepy spider-cult, and the losing combatants had their souls loaded up in the crystals
If you're not good enough to fight, at least you can power a golem! More evidence: when you enter the crypt all the sarcophagies look very classy, and all have warrior like designs on them, some even have weapons and armor (the zombies that came out of them sure do
), suggesting those who died in the fighting pit were honored by the cult and not just slaves killed for entertainment