There is a connection according to some of the comments made by Blizzard Employes. There are two main sources.
"Back in April during a SC2 single player story press event we were at, we asked a question about what is going on with Samir Duran – when playing the game all the sudden there was this guy who’s name was Duran spelled backwards. So is there any connection between Samir Duran and Dr. Narud?"
" * Laughter * That is an interesting question. Yeah, I think it’s safe to say there is a connection between those 2 gentlemen. And certainly the story they are a part of isn’t only not done but is just now getting started. I think it’s very exciting that there is stuff that has been in the works for the background of this universe for many years. Many years in our world, and many many years in their universe that are really going to start to unfold now. And really, it’s all really going to be coming to the forefront in the next few years."
Here is the full interview if you want to read it.
At BlizzCon 2011, the story panel said that Samir Duran and Emil Narud may be the same character. Upon inquiring on whether he appears in StarCraft II: Heart of the Swarm, Chris Metzen commented "You might have met him already. You totally did, by the way."
Based on the above comments it seems like Samir Duran is Emil Narud as we apparently met him in Wings Of Liberty. The only logical conclusion is that Samir Duran == Emil Narud. Although this is all based on developer comments and no factual proof.
If you want more information about any Starcraft Lore I suggest looking at the Starcraft Wiki. It does a tremendous job of fleshing out all the details from the games and the novels. Here is there page on Samir Duran and Emil Narud.
If you plan on reading any of the books I would suggest staying away from it though as they contain massive spoilers on most characters and their back-story filled out by the Novels.