Originally posted by xrayvision
I don't think she knows anything about the adoption agency, but she did overhear Jonathan and Lionel talking about Lionel's involvement in Clark's adoption in a flashback shown in Suspect.
The only way she won't find out is if this show ends before TPTB expect it to. This has been the huge revelation that they have been holding back, and there's no way they won't do it. I say it will happen in S6, probably midseason.
I don't think research on Brainiac (the ship) will be able to reveal anything on Clark, unless Milton Fine tells her. There really is no paper trail to follow Clark's origin. Lex or Lionel would have found out that way if that was the case. Their interest has been much greater along with their resources and time spent. It would make Superman's future #1 nemesis look like a dullard if she finds out like that and he doesn't. She has enough from her memory to be able to figure it out:
-She knew the people at the Atlantis nightclub referred to him as Kal & that the Kryptonians were looking for Kal-El
-She knows that "their world is their poison" and that Clark always got sick around her necklace and other sources of green kryptonite
-She knows that he had a reaction to what she thought to be a silver meteor rock, that like the green rock, was alien in origin
-She knows he was adopted shortly after the meteor shower
-She knows he came back to life
-She knows (if she spent any time in the cave) the symbol burned into his barn matches some that are in the cave
-She saw his geneology project in Rosetta and how his family crest on that paper was the same as the symbol on the stone she stole from Jason
-She admitted that she believed the stone mentioned above was meant for Clark
-She knows that Clark took care of the Kryptonians whereas nobody else could have
-She knows that the freaks from Mortal referred to him as a legend in Belle Reve & heard people talk about his powers (Van McNulty said he caught a bullet, Tina-as-Whitney said he's not what he appears to be, Perry White spoke about his powers)
-She knows that he was somehow involved in how she survived the tornado
-She knows that certain freaks' powers (like Desiree Atkins from Heat) had no effect on him
-She knows he had extraordinary powers in Splinter (she should not have just shrugged this off after everything she's seen)
-She saw him come back to life without the re-animator serum that was needed to bring people back from death in Void
-She has seen him there one second and then completely disappear the next (in Rush, Exile, Covenant, Cyborg, and probably more) and likewise she saw the Kryptonians' speed in Arrival
So either she pieces all these things together, or she will witness Clark in action or perhaps witness his weakness to kryptonite. I think the thing confusing her from putting it all together in her head are those times when Clark had no powers (Perry, Leech, Mortal, Hidden, etc).