He was apparently killed by Kabal. In Kabal's bio he says he tracked down Mavado to kill himand then says it feels good to have his Hookswords back. And in the background of his bio pic they show Mavado dead.
Well, in the Kabal's bio doesn't say that Kabal got his hookswords back... only got hookswords back, but doesn't say that these hookswords are the same that Mavado took him.
Mavado is thousand times better than Kabal... and I hope that in MK7 Mavado come backs and finally kills the freak-out Kabal.
Kabal did aparently kill Mavado, or at least severly injure him. In his Bio it says Mavado beat him and left him for dead and took his hookswords, and in Kabal's alt bio it says he tracked Mavado down and and wanted to kill him, them says "it feels good to have my hookswords back in my hands" as the picture shows them covered in blood and shows Mavado in pretty bad shape on the ground.