Interesting but I think not for the following reasons, let me know if you want scans to back these up:
1) I dont believe he disappeared. If that was the case then what would be the point of giving Itachi his eye and then making it look like his eyes were gauged out? He was never going to be scene again so why not keep the eye and just leave?
2) If he had used his MS before giving it to Itachi then Itachi would have noticed that the MS would/could not activate, but rather it would be stuck in its 3 tomie form for 10 years. Itachi would have noticed this and suspected something was up. Lastly Shisui's MS does NOT deal with memory loss/alteration. I dont know why people think this, his MS makes you follow any command he gives you, as long as it is doable in reality. If I told you to forget the last 10 years of your life would you be able to do that? So then how does his MS change anything? If I told you to protect Konoha you WOULD be able to do that.
3) Shishui gave Itachi his eyes after killing himself. Wait, did you just say he faked his suicide prior to giving itachi the eyes? How did he fake this suicide without leaving a body? Especially given the fact that he wanted to make his eyes look like he destroyed them prior to commit suicide so people wouldnt go looking for them it wouldnt make sense for him to go through all that trouble if he wasnt planning on killing himself but only to fake a suicide...
4) You end by saying that perhaps Itachi destroyed Shisuis corpse.... you do realize that that statement completely undermines your entire thread? Right?
Read the manga man....when the police force came to question Itachi about the CONFIRMED death of Shisui and he fought them, then kneeled to apologize sasuke witnessed his eye change to the MS, that's when he questioned his dad on the different levels of sharingans, so clearly he had MS at time of Shisui encounter....I think you should re read a few chapters man...
Atleast someone other than me noticed... scrolling down and seeing so many people saying "Good job" or "nice theory" was driving me mad... thought this stuff was common knowledge.