as long as you don't go online on cfw since that gets you banned fast, you should be good to go.
That's not fully true, installing nps/xcis of any kind and going online on the nand where they got installed gets you banned.
Using romhacks or cheats in online games can also get you banned, as well as other ways of negatively affecting the online service for others.
But just going online in cfw is relatively safe, and atmosphere with default settings is designed to be used online by the devs.
I didn't boot ofw in years by now, while regurlarly playing games like splatoon online.
I would probably just suggest to disable prodinfo blanking on the online nand and maybe set a different theme on sys and emunand (light vs dark on one of each), to make it easy to identify them.
Sadly the easiest way of changing between emu and sysnand is not working on newer switches, so to switch between sysnand and emunand you will always need to reboot to hekate and then select whatever you want to boot to switch between them.
Reboting from Linux seems to have a way to select a target to reboot to though, so rebooting into sys or emunand should be possible from there.
Also in case you only want to use homebrew and Linux via modchip, I would probably suggest to keep the setup as simple as possible and don't setup an emunand at all, and only use syscfw. Best probably also directly from the github, and not from some package in this case, since many packages use setting different from the default, and are designed to be used for piracy,not online usage.