I'm of the mind that he used it up on something. Like keeping the Deepness under control and since he died, he couldn't feed it any more atium and thereby it grew more powerful.... I don't know, maybe not, but I do think it's gone because he used it on something.
I've been wondering, recently, why atium is so special. It's the only metal Brandon made up for Mistborn, it's only produced in one place--and its a very peculiar place, at that. It seems far too unique to just be used for... Allomancy.
I've also always wondered about how the Lord Ruler keeps Ruin under control. In WoA, Vin describes its power like you burn it away in an instant and then it's gone. Well, obviously, the Lord Ruler didn't do a very good job--Ruin is still prevalent (though you can't exactly 'defeat' a force of nature, not totally). The point is,
after he burned the Well's power away, there was something he was doing by simply existing that kept Ruin/Deepness away.
Using atium could be how he does it. I understand others' concern about the Lord Ruler's control over the economy, but in reality, he doesn't care. That's the whole point of MB1, to show that this self-proclaimed "god" isn't a god. He's not incredibly smart or anything, he just has lots of magical power. He lets house wars go out of control to keep the nobility in check. His obligators see everything that goes on. He has plenty of control to go around.
Plus, having him stave off the Deepness gives him quite a bit of control in the world, you have to admit.
I agree with charity, there could still be some atium as a cache, but the Lord Ruler wouldn't need all of it. No way. He's been using it.
I know it's speculation, but it just makes so much sense, especially showing the spikes with blood on them? Why would EUOL show this to us, and have Sazed think how it looked just like an Inquisitor's spike, then show all the dead and mangled bodies? EUOL even has Sazed speculate how Marsh hasn't really been specific about how Inquisitors are created, and the Marsh seemed "different". He even just up and disappeared the next day, after conveniently showing Sazed Kwaan's writing while not giving him enough time to read the whole thing. There didn't seem to be any other purpose for going there.
Marsh was looking for something, actually, but didn't find it.