According to http://www.imperial-library.info/content/loveletter-fifth-era-true-purpose-tamriel, Twice Vehk broke the C0DA when he returned.
So yes he will return, its prophesised by a letter from the future.
On the other hand, it's possible to interpret the Loveletter as some bizarre form of pro-Vivec propaganda. The bit about "Know Love to avoid Landfall," which reminds me of a passage from the Sermons of Vivec: "I shall keep it [the Ministry of Truth] there with its last intention intact,
so that if the love of the people of this city for me ever disappear, so shall the power that holds back their destruction."
In other words, behave yourself, kids, or bad [censored] is going to befall you.

@ the OP - it's not exactly clear what happened to Vivec in the first place. The "kidnapped by Daedra" line in Oblivion is likely a way to cover for the fact that you may have killed Vivec during your MW playthrough, or you may not have. What's implied in Oblivion is that no one knows what happened to Vivec, his kidnapping being just a theory.
He could have been killed by the Nerevarine, in which case chances are slim he'll come back. Or he was kidnapped by Daedra, in which case who knows. Or, if you take http://www.imperial-library.info/content/trial-vivec as part of the canon, Vivec kicked Azura in the face at some point and ran off...somewhere. In which case he could be back, but again, who knows.

EDIT:
Some questline involving breaking him from Azura's grip would be a good start. If they wanted to make it a bit deeper, they could have the player help Vivec learn to deal with his dwindling immortality and eventual loss of Godlike powers from the Heart's destruction. Maybe he could even give the player the option to end his life if they lead him to think he can't live without them.
Difficulty: it's been 200+ years since Vivec lost his immortality during the events of Morrowind. Even assuming he's around and not dead, kidnapped, or off achieving CHIM or whatever actually happened in the Trial of Vivec (

), I would be
very surprised if he were still alive by the time Skyrim takes place.
His god-powers were pretty well drained from the lack of access to Kagrenac's Tools in the years prior to Morrowind, and from having to maintain the Ghostfence all by himself. (Since Almalexia was too busy going nuts and Sotha Sil was busy being a Socially Awkward Recluse Penguin.) That's why he's in total seclusion by the time the Nerevarine gets to see him. He literally doesn't have the time or the energy to go out among the people or run the Temple anymore.
Assuming he was able to hang onto any power following the destruction of Lorkhan's Heart, I'm betting it wasn't much, if at all.
...Plus he seems pretty at peace with things if you go to talk to him after finishing the Morrowind and/or Tribunal MQs.
Spoiler "It is all very sad. But death comes to all mortals -- and we are all mortal now. In time, death will come to me, Nerevarine -- perhaps even at your hands. It is futile to deny one's fate."