Bear in mind that the person watching these tapes and writing these transcripts was Casper's mother. She had a vested interest in protecting his privacy as much as she could.
In this situation, it's consdered standard practice to apply a pseudonym because the case files exist for governmental view. It's their way of balancing children's privacy with a systemic requirement to have oversight on what would otherwise be entirely confidential documents. Standard rules of confidentiality don't really apply.
James was given a fake name, and so was everyone else he mentioned. Nathaniel is not Casper's real name. Just the pseudonym he was given in the session report afterwards to protect his identity.
He's Caleb's handler. Caleb told them about him. The structure of the organization stops Caleb knowing who anyone is beyond the people he has direct contact with. But, this is his handler, the person Caleb interacts with most directly.