Itachi definitely knew.
It's not hard to figure out that they were related, anyway. (blonde hair, blue eyes, summoning toads, etc)
blonde hair, blue eyes... sure.. but the summoning toads part, that part came from jiraiya.. jiraiya taught both of them.. itachi's been one of the smartest characters in this manga.. he knew exactly how to drive sasuke to hate and kill him.. he knew that sasuke would buy the story about taking his eyes to just to infuriate sasuke further.. he knew madara was gonna get to sasuke, so he planted amaterasu.. and he might have given naruto a power.. of course that could have been the frog scroll.. who knows..
but yea, itachi=know-it-all genious
sh*t.. whos to say minato and itachi werent buddies back then..
minato: itachi-san! how's my favorite anbu?
itachi: disappointed, i can't find a cream to get rid of these stupid stress lines.. hows it like being hokage?
minato: incredibly boring, but i get free ramen! so it evens out!