She's not an "it"!
Spoiler ShowAfter finding out about Quadratum and "unreality", it made me think about The World That Never Was. The name specifically suggests that it was a world that never existed. Sure, it fits the nobody/existential themes of KH2 and the Organization, but what if it really is a "world that never was" as in a fictional world? There are some aspects to it that are similar to Quadratum. It's also very interesting that it's a giant city that's empty that happens to exist in the realm between. You also first access it via the simulated Twilight Town (another "fictional world").
Since Xehanort was aware of unreality before KH1, Xemnas must have been aware. Yen Sid says that the ancient keyblade wielders travelled over to unreality, which means that Xehanort must have been looking for them (since he needed keyblade wielders - IE why he threw Kairi into space). Now we're only thinking about our side of things, but what if the ancient keyblade wielders sent an entire world (or fragment of a world) over from unreality to reality to hide in? What if Xemnas came across them in The World That Never Was and killed the ones that didn't agree to become nobodies, forcing Lauriam, Elrena, Demyx and Luxord into nobodies?