Difficult to say.
C'Thun's carcass was left rotting in Ahn'Qiraj, and still contained enough dark power to mutate Cho'Gall from a
regular two-headed ogre to
this monstrosity, as well as whisper insanity to anyone who got too close to it.
Y'Shaarj was said to have truly died, but his heart still oozed black blood and corrupted everything aound it, and when the heart was revived in the life-giving waters of Pandaria his consciousness appeared to revive somewhat as well, whispering to people and so forth. In the end though Y'Shaarj appears to have disappeared entirely after Garrosh drew all of his heart's power into himself and then was defeated.
There's references to them being outside the cycle of life and death, and destroying their body just seems to slow them down until they can rebuild it or find another one.
If that's the case, then who knows what C'Thun and Yogg-Saron are up to at the moment.