The main reasons someone should use emunand in my oppinion are either, to have all backups and roms in a safe place, where you don't conenct to nintendo from, or if you are one of the few people with a patched erista switch that has a low enough firmware to use software exploits, and you want to have a current emunand to go online with.
For people not planning to use XCIs or NSPs in any way, and modding the switch just for homebrew like sys-dvr and sys-clk or retroarch, I would probably even suggest only using the sysnand. It makes it simpler, while atmosphere is mostly build to be used online. Also it allows to just use atmosphere releases and drop them on the SD, without the need to use any update packs that might contain unsafe thigs.
Some mention brick protection, but with normal use there are not that many things a user can do to accidentally brick their switch, and a backup always helps there. Unless maybe someone develops homebrew themself and experiments with the nand or
downloads and installs a fake rom containing malware.