1. Literally just from system settings menu in sysnand. Before you press Yes to format you take out the SD card so that no data is lost (as your emunand shares data with your sysnand it would be a shame to lose emunand's data.)
2. I only have O3DS and rxTools is the best for O3DS. rxTools also supports N3DS but a fair bit of features don't currently work. Maybe more features have been made functional for N3DS in recent nightlies, but I see people generally recommending CakesFW or ReiNAND for N3DS.
3.
4. CIA = CTR Importable Archive
https://3dbrew.org/wiki/CIA
Anything you would install through DevMenu/BigBlueMenu/FBI, be it games themselves or game updates, or system titles, come in .cia format. I don't know how to find out which firmware version is required for game updates. Lists might be available online but I haven't been able to find any.
If a game update requires 9.6 or higher then the game won't be able to run so that's an easy way to tell.
I don't know if there are fw-spoofed .cias of game updates available online, I've only rarely seen people complain about games not working because their latest update required 9.6+
There must be a way to spoof the firmware properly so that any game or update would work even if it requires 9.6+ but it seems the only way people have gotten it to work was to modify the .cia itself, so... If fw-spoofed game updates aren't already available for download on the usual download sites then I could probably make a tutorial on doing it yourself.
5. sysupdater's an app to install, yes. It comes in .cia format and you install it through DevMenu/BigBlueMenu or FBI.