A ZPM is basically a battery to the Ancients. They have a giant city that relies on them. Surely Atlantis at some point had the potential to pump them out to remain self contained while fighting the Wraith. It's a full city, so they no doubt had the space for it.
I can't imagine the ZPM factory being any more compact than the other equipment they left behind (which seemed to pretty much all of the major equipment for the functioning of the city), so can we assume that the equipment is still on Atlantis, undicovered? I'm pretty sure there was still a large portion of the city left unexplored even after 5 years, so it's possible. They've never explained how ZPMs are created (as far as I recall), so this is all assumption on my part.
I can't imagine the ZPM factory being any more compact than the other equipment they left behind (which seemed to pretty much all of the major equipment for the functioning of the city), so can we assume that the equipment is still on Atlantis, undicovered? I'm pretty sure there was still a large portion of the city left unexplored even after 5 years, so it's possible. They've never explained how ZPMs are created (as far as I recall), so this is all assumption on my part.