I don't think he is saying that. As I said in my other comment here I think he is just drawing a potential parallel to other historic work that was done in a private(secret) domain. The larger point is we simply don't know so it's best to act in a way that even if it hasn't been done already it certainly seems like it will be broken. Hence the move to Post-Quantum Cryptography is probably a good idea!
Aaronson says:
> This is the clearest warning that I can offer in public right now about the urgency of migrating to post-quantum cryptosystems...
That has a clear implication that he knows something that he doesn't want to say publically