Some people still don't understand what Emunand is. It's a sandboxed environment, whatever you do in there is quarantined - so it's a safety precaution. When you update your firmware, the emunand's firmware gets updated. The sysnand's firmware can remain the same forever and Nintendo will never find out what your real firmware version is.
If you want to go online it's still kind of pointless. (Unless you are willing to update your sysnand too)
Nintendo might be able to detect if you are running an emunand if you go online while in emunand. So even if you aren't running personal backups or pirated ones, you could still be banned just for being in emu. (Maybe they won't be able to detect this, we have no guarantee either way).
If you wanna keep sysnand on the lowest possible firmware so you have more potential exploits, you won't be able to use the actual sysnand to go online, update games, or play any games beyond your current fw.
Using a jig and dongle/phone/PC every now and then (leave the console in sleep mode) is just not that big of a deal. An exploit that you can run by simply booting the console would be great, it is just not a big enough of an inconvenience using Fusee Gelee to care about it.
If you are gonna keep both nands up to date, than I can understand the use of emu as a 100% offline system for homebrew/piracy. While using sys for online play and genuine games.
Bear in mind that we also have no guarantees that Nintendo won't be able to detect even on the sysnand that an emu has been used on the console due the apparently recorded logs. The logs may also (not sure if confirmed) keep track of the number of times a console enters RCM. Maybe they will just ban all consoles that enter RCM more than a set number of times as it's a very good indicator that you are probably "hacking" your console.
This is a time will tell situation.