I have been following the guides on Reddit since the 10.4 update was released, updating the NVer and other system titles to keep online services functional on my 10.3 3DS. (They refer to this as creating a "Frankenfirmware".) And I wanted to mention that I've never had any issues after installing the .cias mentioned in the guide you link, so you should be perfectly safe installing them provided you follow the guide exactly.
That said, there are some things about Frankenfirmware that you might benefit from knowing. Updating the NVer to the value of the latest system update (or greater) is what allows you to use applications that require you to log into your Nintendo Network ID, such as Miiverse, Badge Arcade, and the eShop on outdated firmware. Some games may also require the NVer to be current to function. (Mario vs. DK: Tipping Stars is one example, and it's likely because the online is so integrated with Miiverse). Also, you will still need to access the eShop in particular through the HANS homebrew. Updating the friend module title mentioned in the guide is what allows you to view your friend list, play most 3DS games online, and use the official Pokemon Bank on outdated firmware. Unfortunately, even with these two titles (plus the eShop ones) updated you still can't utilize certain tools on the system, like the Save Data Transfer Tool and the system transfer. Of course the former app is pretty pointless if you have any homebrew save manager.
I'm not sure what your circumstances are exactly (you have 3 3DS systems mentioned in your sig) but if you were interested in following that guide you linked for any of them, I hope the info I gave was helpful. For future updates, you can check the site with update info linked to in the guide to determine if any of the 4 system titles need to be updated. After a new system update is released and the exact details are determined, the report for your region should show exactly which titles were changed in the update, and the new versions of those titles. I would refrain from updating any titles other then the 4 in the guide, as doing so may very well cut off your access to certain exploits.