1) Agent 47 is the main character in the "Hitman" video game series. The games have Agent 47 carrying out assassinations, mainly for money. 2) Probably a joke on how your boss seems like the type of woman who has actual skeletons in her closet. 3) The name "Karen" has become somewhat of a slang term for rude, entitled women who are quick to call for a manager or corporate to complain when things don't go their way.
Does that clear things up?
I can explain all three references to you! 1) Agent 47 is the main character in the "Hitman" video