Think about it a little.. If he used Shisui's eye for Izanagi. Then the eye closes. He can't use it for Shisui's technique. Once or another,don't you think??although Shisui's eyes were normal sharingan at the Kage summit that guy with the Byakugan said Shisui had the power to manipulate others mind without letting them know about it. So in Shisui's case though he has the normal Sharingan but he had a unique power and also his chakra i guess is sort of special thats why Danzou also took his arm. So what i'm saying is Danzou could have used Shisui's eye for Izanagi but the most like scenario is either he is really dead or he escaped somehow controlling Sasuke's mind with Shisui's eye.
In the manga he states that he was planning to use it in Madara not in Sasuke..
If he had used Shisui's abilitie do you really think Sasuke would have stab him with Chidori anyway??