Some say the Nerevarine killed him.
Some say he was taken by daedra during the Oblivion Crisis.
Some say he Zero-Summed.
Some say he dwells yet still on another plane of existence, biding his time until his return.
So some say.
Vehk's an [AYEM]hole. He's always been an [AYEM]hole, from the moment Nerevar found him in a gutter and took pity on him. He killed Nerevar, his friend and benefactor, because he wanted some power that his king knew better than to touch.
He puts on his pretty-face when he's talking to the Nerevarine because he didn't get to where he is by letting everyone know just how much of an [AYEM]hole he is.
I think the Tribunal were right in stealing the heart's power. They brought a lot of good unto Morrowind because of it. Good that would have been lost if Nerevar had been so stubbornly faithful to a daedroth who cared not for the fate of his people.
Don't get too dreamy-eyed over the horrible Hortator. He wasn't a nice person either.