I agree that Raiden should stop receiving visions now that the possible threat of Armageddon has been eliminated, because those visions weren't just any visions. I believe that those visions were directly related to preventing Armageddon and only Armageddon, and since that threat is indeed non-existent now, there's no reason for him to receive visions, since their purpose would be trying to prevent a threat that doesn't even exist
Yes, there's still Shinnok and Onaga to be concerned about, but those threats were going to happen regardless of Armageddon. There was no way to prevent those from happening; those are seperate events that were already set in motion long before the most crucial period in time to prevent Armageddon (the MK1-MK3 period, when Shao Kahn was in his prime). I think when Dark Raiden sent those messages/visions to Raiden, he was much more concerned about Shao Kahn and Armageddon than anything else, and left Raiden to handle comparably lesser threats like Shinnok and Onaga.
Also, Critical. This is just a crackpot theory of mine so take this with a grain of salt since this shit is confusing, but I don't think that those were Raiden's visions so much as Dark Raiden's memories. It's possible that in his haste to send his message to his past self, what was shown was Dark Raiden going through his own memories in an attempt to find the best point in time to send the message to himself.
It's also possible that they were just simply referencing past events in the original timeline while also just showing that they were going back in time with the story. Could be wrong, of course, though, we'll see.
Lastly, about the "change history" part. What history? Unless you're referring to post-MK3 events, but that isn't history now. That's the future/present now, since we're in an alternate timeline that hasn't yet caught up to the original timeline's point yet.