You can actually back up your save files with SaveDataFiler if anything were to happen, but Nintendo can't really tell if you're in EmuNAND or not. Your games are also in the "Nintendo 3DS" folder, so you can always just back that up and your EmuNAND.bin if you're worried about the risks.
If you leave stuff on SysNAND, it might be more difficult to manage everything, but I don't think it would hurt if you did that. It feels a bit counter-intuitive to me, but do what you need to.
I haven't really tried with Decrypt9, but it's probably in the readme. I know that having "NAND.bin" on root and pressing A while holding Up on "Downgrade Console" in the Gateway Menu will do it.