Yes and no. I prefer updating with ChoiDujourNX because it gives me more control on how I update unlike the official Nintendo updates. Also updating your firmware online will always remove AutoRCM meaning I will have to manually enter RCM again if I want to go back to using AutoRCM. You can also downgrade without a NAND backup by using ChoiDujourNX. Lastly, updating officially might not be totally safe with a hacked console since the NAND will likely be tainted, transmitting all sorts of telemetry when you download the system update from Nintendo unless you restore a clean NAND backup before doing so. However even if you do that, you'll then have to make another clean NAND backup since Nintendo believes you to be on a new firmware, a firmware that doesn't match your previous NAND backup.So what you're saying is if I'm comfortable using a hardmod, then I can upgrade and burn my fuses knowing that when I want to run homebrew I'll have to do so using some sort of jig.
However, if I'd prefer a soft mod (deja vu or some other future exploit) it's best to upgrade without burning fuses and backing up my current nand. Is that right?
Tl;dr Its better to update with ChoiDujourNX than officially.