So, really underdeveloped and not very well thought out theory I've discussed with one friend IRL for a short period and that's it, so here goes.
I believe there is (or was) sixteen beads of lerasium. My reasoning:
Confirmed lerasium :
The Lord Ruler had a bead, which is obvious.
The original nobles, nine of them, had a bead.
Hoid has a bead, as confirmed by
Elend has a bead.
So, that makes twelve. Why such a random number?
Uses of sixteen:
Sixteen shards
Sixteen allomantic/feruchemic metals
Sixteen percent drop to sickness
Preservation went to extra work to make sure sixteen was on the list, adding atium and it's alloy to fit.
So, why, after making sure it was a sign, would you only have 12 beads of lerasium?
Why they weren't (possibly) at WoA:
I've got multiple reasons for this one.
The Lord Ruler took them as a reserve, just in case, but missed two
They were taken by worldhoppers
They were being kept, unknowingly, by the Keeper's
The beads were gone during the many years before the Final Empire
They were on the other side of the world, where the southerners are from
The kandra had them, possibly knowing, possibly not.
So, I really don't like most of these ideas. They all have individual problems, which you will no doubt rip apart the entire theory with.
The Lord Ruler took them as a reserve.
So, the problem with this is that when Harmony moved the world around, due to the high amounts of metal, which glowed brightly in the CR, at least to Ruin and likely to Preservation, would hide it. That means that when Harmony restructured the world, it would be "Lost in the move", somewhere random in the world, as a large amount of Kredik Shaw was turned into land. This could have good or bad ramifications for overall plot, depending on how Brandon would theoretically play this out. I don't like it a ton, but this I would prefer to They were taken by worldhoppers and The beads were gone pre-Final Empire.,
They were taken by worldhoppers.
I don't really like this option. Not at all. But, logically, it would make a lot of sense. The Well of Ascension is one of the two ways to travel to and from Scadrial. Admittedly not the safest way, due to Ruin, but still there. So, someone comes in, explores, finds a bead. They take it, whether because they know its inherent value or because they don't know what it is. I mean, it's an easy way to become one of the most powerful people alive, doesn't require anything location based, and to top that, doesn't have bindings, rules. You input metal, output is power. You don't have to worry about losing it, or "ranking up". And while it requires some learning, it isn't memorizing aons or learning soulstamps. That isn't easy, so Lerasium is made all the more valuable. I don't like this for plot reasons, it would mean the extra beads are never factored in to Mistborn again, or will take a while. The only possible good ramification of it is that their children could be allomancers, introducing allomancy to a seperate bloodstream, causing interesting effects come Era 4. I think this is unlikely, because Brandon wouldn't want to spoil Mistborn, so it would have to be some backwater planet, and wouldn't even get atured until Dragonsteel or Era 4, and unlikely in Dragonsteel. So, I don't like it, but it's possible.
The Keepers had them.
The Keeper Synod was killed. Big problem with that one right there. But, think of this. The term Keepers is, obviously, referring to memories. Right? But what if, originally, they kept Lerasium, that they got from anywhere, that matters least, plenty of reasons could be found. They keep the beads, making sure they aren't lost. Over time, those memories fade. It's forgotten, and the beads are just there. Alternatively, as memories are unlikely to fade when it comes to the Keepers, only the Synod knew, a group never seen on screen. The Synod kept it a secret, misleading the Keepers, letting them assume it was about memories, while they guarded the beads. Maybe they were chosen by Preservation, maybe they found records of their importance. I like this one a lot. About the same as the Kandra one, and higher then the rest.
The beads were gone pre-Final Empire.
The Well was there long before the Final Empire, and had those beads. Some wandering person finds the Well, thinks it strange, takes a bead as a trophy. Or four. Or a group comes. Or ancient worldhoppers. Lot's of time, lots of options. Those beads were taken way back then. Maybe given to the Woldbringers, which would explain it crossing it over to the Keepers. Don't really like it, not at all, I can't think of much for this one, and what I can sucks, so this is my least favorite, and one I don't want to see, unless he adds another Era to MB from back then.
The southerners had them.
The southerners, or some other group on the other side of the world, had them all throughout TFE, and still have them. They didn't know what they were, so they didn't eat them, because what rational person eats metal? Or a non-southener group/a single tribe(clan?) did eat them, and masqueraded as gods, explaining how deep their reverence for it goes, more then just Kelsier telling them so. I like it, but I think there is better alternatives.
The kandra had them.
The Kandra guarded huge stores of Atium. Why not a few beads of Lerasium? It could be tied in with TLR hid them, because he had them guard Lerasium on top. The Kandra homeland survived, but if Harmony didn't know what to look for, Sazed wouldn't see them through the metal content, leading to them still being there. And ripe for the taking by Kelsier. I'll get to that later. So, not my best developed one, but this one I really like, as much as the one with the Keeper's.
It was at the WoA:
It's obvious they missed two beads, why not four more? A different part of the room, at the bottom of the pool, rolled into the corner, there is a million ways that these beads could have been lost in there, missed by them. They could even have been hidden better than the rest just in case as a backup plan of Preservation's. So, possible.
Plot ramification:
The Southerners recognize both Allomancy and Feruchemy. They could have been given Allomancy by Kelsier, who found the beads.
A combination alloy of lerasium-atium could be made by anyone, and as said by Brandon might give you permanent Atium, needless of burning.
This might be outdated, but the other thing is a superweapon. Now come Era 4, planet ending might be wanted...
So yeah, that's my few ideas.
What it explains:
The Southener's revere both Allomancy and Feruchemy, what better way to know about Allomancy then with allomancers? And the easiest way to get it? Lerasium.
How there will be a Mistborn in Era 3. They don't need the breeding program. They just need to use some Lerasium, and they have enough investiture. Slightly less than TFE, but still enough for Mistborn.
Why Kelsier was so powerful. It takes a boatload of spikes to replicate all Feruchemy, and even more for Allomancy. He had Mistborn powers, but maybe he had lerasium as well. That makes him the most powerful allomancer in history (Except Vin), more than TLR, and reinforcing that he is a god. He would easily rip the metal out of your body, crush you in your armor, with barely a thought. And it is possible that he couldn't use his Mistborn powers, it had to go to keeping him in the CR, which means he would need it. And it's hinted that there is ways to get feruchemy. So it could be only one spike is there, as an anchor.
So, that went 50x longer then I meant, I'm sorry for the lengthy theory. Now I watch as my hard work is torn apart, courtesy of the Arcanists.