It takes many, many duplicate nodes to appear before you finally get all 40. You need to write down each node you’ve already received that way when you get a duplicate you can simply delete it and use more resonate stems and create another. I’d say you should have around 600 resonate stems in your inventory. That will create 150 nodes. Of those 150 nodes hopefully you’ll get lucky and get all 40. Once you do your emblem upgrades. That’s the completion prize.

You can (and definitely will) get duplicate override frequencies, but you'll always get something out of the Sleeper Nodes: blues, shaders, Braytech engrams, a ship, or a Sparrow. The Data Mine emblem will turn into the Warminded emblem (on my Hunter if you want to see it) after opening all 40 unique Nodes.