With 3ds/2ds prices still through the fucking roof, I have been looking at some Japanese models, since their price tags are slightly less crippling to look at. Unfortunately, I can't speak Japanese, and I haven't regularly used a 3ds since the release.of NSMB2, so id like to have it in English so I can navigate without googling everytime I need to get inside the settings. The issue is, this used to lock you out of a bunch of online features. My question is: with the end of online communication/gameplay, is this still something I need to worry about? I know game updates are normally gotten from the eShop, but is it possible to download the updates manually from something like hShop? What about software updates? (Do I need to install software updates at all since all they seem to do is try to break homebrew?)
To answer your question about system updates, it's almost always safe to update and there's no reason not to update as long as your CFW (Luma) is fully updated. System updates are only an issue on OFW, since the updates are basically just for patching the exploits used to get CFW in the first place.
As for the limitations of region changing, The Guide has that covered on their page for the process.
Another really important thing is that you should never follow any guide other than the one I previously linked. You especially should not follow a video guide because they get outdated very quickly and may promote old and/or unsafe methods of hacking the console.