1) Yes, the Switch theme community is amazing. All theme mods are implemented as patches that go in the atmosphere folder. If anything bad happens and you can't boot your Switch because of it, you can fix it by deleting everything in the following folder:
/atmosphere/contents/0100000000001000/romfs/lyt
2) Right, try to avoid going online at all using emuNAND unless you've cleared your emuNAND's prodinfo, or have set blank_prodinfo_emummc=1 in exosphere.ini, or are using 90DNS or Atmosphere's DNS redirection features to block Nintendo servers. More on that last part here:
https://nh-server.github.io/switch-guide/extras/blocking_nintendo/
You may want to use more than one of these methods simultaneously, just to be on the safe side. This will allow you to keep your Switch online while in emuNAND, which can be helpful for some homebrew, while making sure you don't get your sysNAND banned in the process.
3) Exactly. Use emuNAND for CFW/homebrew/piracy/mods/cheats/whatever. With the proper protections in place, you should not get banned. Note that you won't be able to play online officially while using emuNAND, although you can still use switch-lan-play. Use sysNAND for playing purchased retail games, especially ones that you want to play online. This is the most common, dirty emuNAND / clean sysNAND setup.
4) Yes but only if you take the proper precautions like I listed in part 2.
5) In general, yes, it's safe. And there is a tool called Daybreak that comes with Atmosphere, and you can use it to keep your emuNAND updated as well. Note that sometimes a Switch update will update the firmware on the game cartridge reader. I've seen this break Atmosphere before, but at least when I've seen this happen I've still been able to boot Atmosphere by leaving the cartridge slot empty. Once you've updated emuNAND, it should no longer be a problem. Note that Atmosphere also has an option, called nogc, that allows you to disable the cartridge reader while in emuNAND, if desired.