While I don't entirely agree with this, I think as others said, it was just to avoid displacing the idea that the player's Nerevarine was the real one by divulging any factual information about him/her beyond the basics he did
Whatever the devs decided on regarding the Nerevarine's fate, it would end up pissing at least someone off. Yeah, I guess some people might actually prefer the 'went to Akavir' scenario, but how many? We can't be sure, but my guess is 'not a lot'. It's the easiest solution, rather than the one that makes most sense, hence my comment about 'laziness'.
Nerervarine going to Akavir is merely a rumor, and has no substantial proof, it could easily be a case of mistaken interpretation. There's a game you play in school where everyone sits in a circle, the teacher whispers something in one person's ear, then they whisper to the next person, and it goes in a complete circle around the room between like 20 people, and at the end you find the last person usually says something completely different than the first. Word doesn't travel so accurately via word-of-mouth so I'd just chalk this up to another unsubstantiated rumor.
Why would we hear about it? With the Empire in crisis I doubt anyone cares. Vivec's a much more prominent figure to the people, yet we still only heard rumors about him, nothing concrete.
I think the reason we don't hear about Vivec or any of the Tribunal is because some people actually murdered them, it was left as a choice, it wasn't a specific quest or anything, but you were given the option to kill the entire Tribunal in the game, which the Temple would no doubt cover up by saying they went missing, to reveal that the Gods of the Temple are dead would create a massive question of faith that could erupt into a very serious ordeal.... so of course the Tribunal are "missing".... history will probably be written to assume they ascended into Aetherius or some such nonsense.