If you follow my advice, you will be fine. I can't say anything about the advice of others.
Yes, if you get banned on one, you get banned on the other. The point of an emuNAND is to keep your hacked NAND separate from your clean NAND. For example, if you connect your clean NAND to the internet to play online, Nintendo will not see any of the hacked things you've done, since you hopefully did all of your hackery on the dirty NAND that's kept offline.
No.
- Backups online will refuse to work.
- If you try, you will be permanently banned.
If you are using backups on an emuNAND, that emuNAND should not be connected to the internet (or the whole system will be banned). In that case, ChoiDujourNX is required.
If you are using online play with an emuNAND, that emuNAND should not be used with hacks like ChoiDujourNX (or the whole system will be banned). In that case, you will need to update officially using the system settings.
No. As I said above, the only thing that can burn fuses is updating your sysNAND without AutoRCM being installed.