Never? That's a long time there... He fits the pre-requisits... his name was mentioned in the manga prior to the interview in which it was revealed that Anokata was already in the manga, he's perfectly positioned to lead the assault against the black org, while ensuring that no real damage is done, he can keep easy tabs on the "Silver Bullet" (Akai), and he shares Conan's nickname of "Cool Guy" with Vermouth (and since Vermouth has a "special relationship" with Anokata, the sharing of nicknames does follow suit, and the fact that she's old enough to be her own mother means that she could have known JB when he was younger). Heck, when they first met, Ai said to Conan, "Does he make you feel strange" (No Group, but that's Sality's translation) so it looks like her Black Org Radar had a ping go off... Black is his last name, first name "James", a Holmes fan...
Born in London, raised in Chicago (the city of Al Capone, as he points out when his character is introduced...) he mimics some of the traits of S. Holmes arch nemisis... Born in England, Professor Moriarty is well traveled across the globe. Name of "James" as a first name (which is actually the name of Prof. Moriarty's brother, and then later stated to be Prof. Moriarty's name)... If he used an "air rifle" in the shape of a cane, it would be a slam dunk (almost) that it's him!
If we can just ignore the fact that JB already knows that "Sherry" is Ai (Ch. 435), because that would flat out prove that it isn't him, there is a lot of other evidence that it is him... unless, he has a reason to not just kill her that isn't revealed yet (she is the one w/ the knowledge of the drug, and could be the only one that can explain what happened w/ Vermouth and killing her would lead to Vermouth de-aging into childhood, or the only one that can resolve the age reduction that happened to her and Shinichi... or something).
Still, it's fun trying to figure out who Anokata really is.
To be on topic for this post though, yes, I think that JB does know who Sera is.