I’m sure the CIA knew about his affair, he would have had gone through a rigorous background investigation to include a complete lifestyle polygraph. If this woman was found to not be a foreign intelligence agent or receiving classified information they probably ignored it. Given that this affair ended sometime ago - they probably just regarded it as a personal problem. The question is, why was the FBI investigating thin air reports of harassing e-mails? Who gave them authorization to hack into e-mails and conduct surveillance based off of little to no evidence of criminal wrongdoing or classified information negligence? Isn’t there a FISA court for a reason?