What happens when you restore your NAND backup?
Did you follow the guide? Did you finish it?
https://nh-server.github.io/switch-guide/user_guide/emummc/partitioning_sd/
If you didn't format either NAND, you can potentially move the /Nintendo/ folder to the proper location so it will be read by the emuNAND. Alternatively, you can backup your save with Checkpoint and then restore it on the sysNAND with Checkpoint. While it probably won't dirty your NAND, it should be avoided if possible, and it's your risk to take.
That's quite the price difference. I personally don't think the extra $150 is worth it for an unpatched unit, but unpatched systems are recommended.
If the patched system is on 4.1.0 and has never connected to the internet, then it should be fully hackable. If you are prone to make a lot of mistakes (i.e. Doing things that would brick your system, accidentally updating the sysNAND, accidentally connecting your sysNAND to the internet without PegaScape, etc.), then you should get an unpatched system.
Copy the /Nintendo/ folder to the proper folder so it can be read by your emuNAND.