The thing with Armageddon is that it's not a solid event. It's a consequence of many events.
On the first timeline, it happened 10 years after MK3. But now, with Raiden possible changes on MKX too, he postponed the end.
I already said this once, on Raiden's thread, but I will be more simple: Raiden did not prevented Armageddon. His only signal of Armageddon was the broken amulet, that in truth marked his death, not the end of all things.
When Raiden makes Shao Kahn being judged by the Elder Gods, he simply prevents the existence of Kahn in the same hour, day and year that the thunder god was killed. So, he prevented his own death by taking out Shao Kahn from that exact moment, that's why the amulet fixed, and that's why he thinks Armageddon is prevented.
Armageddon is caused by the numerous kombatants and it's constant threat to the realms, not by Shao Kahn himself. Also, Raiden preveneted Kahn from existing on the battle and winning, what opens the chance of another one winning the battle against Blaze.
We clearly see that we have more characters and moe kombat. There is no way to escape the apex of destruction, even if they survive, but the moment will come.
About Shujinko, I really hope he appears because I want Onaga on this game.
Raiden experienced Shujinko, but wasn't present and didn't know at all the events that led to the Dragon King's ressurection. He only knows Shujinko did. He will need to find Shujinko to prevent Onaga's return.
Sorry, Thunder God, you're one of my favorites, but this time I will seek your failure, I WANT ONAGA!!!!!!!