Shishui either gave danzo his eye, or he sent root to take it , the 2nd one makes little sense because, why would danzo leave him alive with 1 eye afterwards? he could report what happened to the third hokage, which would get danzo in serious trouble...
Shishui and danzo had similar beliefs (protecting village from the shadows) , which leaves me to believe he gave him 1 eye, itachi the other
His body? Uchiha police had it , found it at the River with a suicide note....after inspecting the body , cause of death was drowning , Kabuto is unable to find the body after that