Board Thread:Theories and Speculation/@comment-1783334-20150507053750/@comment-1210805-20150508095658

Nope. They've always been very explicit about Shisui's body never being found. The only reason anyone knows he drowned himself is because of the suicide note. Not even Kabuto, the expert corpse finder could find him.

As for motivations, well, maybe he thinks Itachi made a mistake by letting Sasuke live. Perhaps Shisui believes that the existence of the Uchiha will inevitably lead to problems.