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> pretty sure this is stems from the insane US legal requirement to not export SSL technology to enemy countries

This is most likely OFAC. Lets Encrypt could apply for a license to do business with sanctioned entities, and given their use case it would most likely be approved.

https://ofac.treasury.gov/ofac-license-application-page

OFAC regulates commerce, not speech. Let's Encrypt is not doing "business", they're operating a free informational service. Lots of organizations interpret any information exchange as subject to OFAC regulation, and you and Let's Encrypt have good company in this interpretation, but I think it's unnecessarily ceding ground.
The government may use as wide of an interpretation of commerce as they can get away with. We've seen this happen before [0]. Sure, Let's Encrypt isn't taking money from the entities they offer certificates to. But the OFAC desk jockey assigned to that case only has to concoct some sufficiently plausible-sounding trail of money connecting the backing 501(c)3 and a sanctioned entity in order to levy penalties, and the legal team will not like that risk, even if it's unlikely for OFAC to win on appeal in a court.

[0]: https://en.wikipedia.org/wiki/Wickard_v._Filburn

This is true, of course, and I understand why some companies don't want to take the risk. But I would hope that Let's Encrypt would take the opposite stance. They were born out of the EFF and have EFF & ACLU board members! These orgs live for this type of legal fight.
Wasn't there news a bit ago about some people being suddenly excluded from Linux kernel development for presumably similar reasons?