It's merely speculation but I think it's plausible:
If some random journalist was able to decode the dots, the NSA probably decoded them too because why not.
The fact that they know how many people printed this document shows that they keep detailed printing logs so they shouldn't have trouble finding out who exactly used this specific printer at this specific time. And if you think about it, this is exactly what they should be doing instead of relying solely on weaker evidence.
Then they searched her work computer and got some more evidence (the e-mail contact, maybe more they aren't sharing).
They presented whatever evidence was sufficient to convince her and the public that they know it was her, she doesn't seem very tech-savvy, freaked out, told everything and now it's done.
It's merely speculation but I think it's plausible:
If some random journalist was able to decode the dots, the NSA probably decoded them too because why not.
The fact that they know how many people printed this document shows that they keep detailed printing logs so they shouldn't have trouble finding out who exactly used this specific printer at this specific time. And if you think about it, this is exactly what they should be doing instead of relying solely on weaker evidence.
Then they searched her work computer and got some more evidence (the e-mail contact, maybe more they aren't sharing).
They presented whatever evidence was sufficient to convince her and the public that they know it was her, she doesn't seem very tech-savvy, freaked out, told everything and now it's done.