There was a reference to this in the scene with Lex Luthor in Superman's ship in Batman vs Superman (where Supes died). I honestly only vaguely remember it though (seriouslyl? Do I have to go back and rewatch that one too?).
Reasonable headcannon, but yeah, not stated anywhere in the films (er... maybe suggested in that bit in BvS?).
Yeah. Hence why one would have to speculate some sort of previous kryptonian intervention at some point. Maybe...
It's actually interesting though that while the Synder Cut has a boat ton more of the villans talking about the mother boxes and their importance, it's actually only in the Whedon Cut that the focus is on the humans and discovering the motherboxes and their importance. The Snyder Cut more or less ignores the whole bit about Lex being exposed to the boxes and info in Superman's ship (or wherever he was, since my memory is hazy). Lex is completely ignored in the Snyder Cut until the end credit sequence. But in the Whedon Cut, Bruce is actively investigating the motherboxes (though he doesn't know what they are) based on the insane ramblings from Lex Luthor. This is stated in the film. He then notices a mural with three boxes on it on the back wall in the fishing village that Aquaman hangs out at, and that spurs his investigation more. There are other bits of information about them gathered throghout the Whedon cut that allows the heroes to learn what they are and their importance (including Cyborg and his dad filling in some info as well).
In the Snyder Cut, none of this is present. No mention of Lex's drawings of the boxes. No boxes drawn on murals. Just Hippolyta sending the arrow to warn Diana, and then a strange scene (which is not in the Whedon Cut) of Diana finding some chamber under the temple in Greece, which contains ancient drawings about the mother boxes. Diana apparently doesn't know what they are and has to learn about them, despite an entire contingent of Amazon soldiers (and an entire building on their island) dedicated to its defense. I guess she just didn't pay attention during history class? But anyway, that's how they learn about them in the Snyder Cut.
In the Whedon Cut, Diana already knows what the boxes are (at least the history of them, which actually makes far more sense). So when Bruce comes to her with his investigations and discoveries, she just fills him in, and then informs him that one box has already been lost (cause she just saw the signal arrow shortly before). The flow of information about the boxes actually works better in the Whedon cut than in the Snyder one, IMO. I suspect Snyder got so caught up in having his villains monologue about them and using that to inform the viewers about what they were, that he kinda left the whole "heroes have to figure this out" as an afterthought.
Again though, despite much more actual screen time spent involving the boxes, Snyder's cut was less coherent and paced than the Whedon cut. The audience gets the exact same info, but Whedon has it occur as the heroes learn and discuss things, so he's covering both sides of that requirement at the same time (more efficient use of screen time). It's little things like that which make a huge difference in the result.
BTW. I am in no way saying that the Whedon Cut of JL was a great film. It had some signifcant problems as well (as the box office numbers attest). But, IMO, it was a far better put together film than the Snyder Cut. it was certainly a far far more effcient use of my time from a "how much story did I get vesus how much time I spent getting it?" pov.