Ok now the thread is going from one broad leap to Kakashi having Mangekyou to everyone putting words in Kisame's mouth. Kisame never said that Itachi shouldn't use it because it strains his eyes. He just warned him against using it too much, we have seen that same warning given to people throughout this show and it was because of Chakra consumption i.e. Kakashi telling Sasuke he could only use the Chidoro twice. Making the leap that Kakashi would hear this and decide on the move damaging eyesight permanently is crazy. There's no precedent for that kind of warning meaning that anywhere else in the show. The closest thing was Lee's Lotus use back in the day and that was still not permanent damage. They show the flashback to what Kisame said as proof of Kakashi's statement about the Chakra requirements of the move.


Kakashi knowing about the eyesight deterioration is a self-contained statement that we can do nothing but speculate about. Kakashi having the Magekyou is one explanation however the other possibility, that noone has mentioned, is Kakashi found the hidden Uchiha scroll that explains the technique. I don't remember them showing Sasuke taking it with him or destroying it so it was probably still right there waiting to be found.