Limit to how many times a particular scanner can be used

Some of the blueprints' text descriptions indicate that those are the best you can find for that function (e.g. mining laser combat effectiveness). Additionally, if you view your suit/ship/multi-tool inventory, the 4-swirl summary on the right shows how much you've upgraded various aspects of that thing (e.g. mining, combat, scan, grenade). So, if you apply all the blueprints you have but the swirl isn't full, that would seem to indicate you're missing some blueprints.

I've been getting duplicates for (literally) days now, but I've never found a blueprint for my ship's scanner. It seems silly that there would be a category for such a thing if there were no blueprints for it, so I can only assume it comes along later in the game. Same thing with the "Curiosity" section of the product construction menu -- there's nothing available for me in that section yet.

But just because you're getting duplicates doesn't mean you should stop grabbing them. (Though you could probably stop grabbing the multi-tool ones from the wall units ...) After dozens of dupes I recently found a product blueprint that allows me to make a boatload of money relatively easily. It's possible that it only dropped for me after reaching some milestone, but if so I have no idea what that milestone might have been. I've just been wandering around.

In order to obtain the Atlas Pass V1, you need to encounter a Space Anomaly. It will be extremely obvious when you've encountered one, as when you warp into a system with one in you'll see as you're exiting warp.

Inside an NPC will give a simple test for a milestone, then give you the blueprint for the Atlas Pass V1.

Once you've obtained that, you can start finding Atlas Pass V2 and V3. The fastest way to do this is to use a Bypass chip with one of the Orange beacons on a planet, and select 'Colonial Outpost'. Keep doing this until you get a waypoint for 'Manufacturing Building'. This type of building requires you to break down a door to enter. Solve the puzzle inside and you'll be awarded with a blueprint, which has a random chance of being an Atlas pass. The Atlas Pass V3 will allow you to enter V2 doors, so if you get the V3 before the V2 it's fine.

You do not get the Atlas Pass V1 from an Atlas Station, only Space Anomalys