Remember Dr. Williams, the Chrysalis scientist who went to work for Khan? He was one of the senior scientists on the project, surely he would've known about any hidden embryo caches. But he never brought them to Khan's attention, which IMO he would've done to further cement his good standing with the dictator.
Maybe he was hedging his bets by keeping them secret. Or maybe he didn't know about them because they were a secret Dr. Kaur kept from the rest of Chrysalis. There are many possible explanations.
And
King Daniel's right. There are plenty of contradictions already extant within Trek canon, and the only way to reconcile them is by not obsessing over every exact detail. That's the nature of any lengthy, evolving narrative, especially one created by multiple people. Sometimes you just have to accept that a new work requires reinterpreting things from an earlier work, and you can't do that if you're unwilling to ignore a few details here and there.
Hmmmm....I have to say, I'm more the opinion that once the timelines diverged (whether due to Nero's appearance or not, though I'm more inclined to believe it was already different), events in the past caused by events in the future would no longer occur, because that future no longer happens in the new timeline. So you wouldn't have things like the Ferengi crashing at Roswell in '47, Kirk and co. appearing in 1986 in a Klingon BoP and rescuing two humpback whales, the Borg attacking Earth in 2063, etc, etc.
This isn't a matter of opinion, it's a matter of logic and physics. What does "no longer occur" even mean in this context? "No longer" means "after a change." But "after X" means "in the future of X." How can the past be in its own future? It's a contradiction in terms to say that the past "no longer" happened the way it happened. From the time traveller's subjective viewpoint, it may appear that a single moment can come before or after itself, but that's an illusion caused by the traveller doubling back on one's worldline.
The only way there can be two versions of a single moment in time, by definition, is if they are simultaneous, in parallel timelines. But in this case, we're talking about a single timeline that forks into two branches in March 2233. Anyone in either of those branches travelling back in time to a date before 2233 will end up in the same timeline. And therefore it follows that either one could affect events in the other. And as I explained, we have multiple canonical examples of exactly that happening.