i am pretty sure he used KA on kabuto's mum, so I think he already had shisui's eyeplot no jutsu.
or his lost his real eye in a battle or war.
Has I said, shishui was only a child and when he was an adult he fought Ao and he had both his eyes, so that theory doesn´t make sense.He probably already had his eye
i dont think itachi killed shisui. he said he did when he told sasuke about shisui. but as far as i know shisui just gave the eye to itachi and died some other way which is still a mystery.Itachi killed Shisui an Danzo took one of Shisui's eyes. Itachi put the other in the crow he implanted in Naruto.
Danzo had it covered, because he can't turn it off (like Kakashi) and it'll take up unnecessary chakra. Also, he couldn't be seen with a Sharingan :|
LOL xDMaybe he always had a thing for jacking sharingan's?