Yes, EmuNANDs are protection. While in EmuNAND it's like a completely separate Switch. In fact, you can have as many EmuNANDS on many SD cards. I made separate EmuNANDS for Kids and for Adults. That way I keep my save files safe and I can have kid friendly games only for them.
I would also like to point out that the EmuNAND space is not wasted. You can install to it. The majority of it will be used by your games.When in EmuNAND if you install to System you are installing to the EmuNAND. IIRC about 2GB is for the system files. The remainder is used when installing to EmuNAND.
Plus you can shrink the EmuNAND.
I use 6GB for SXOS. I only use it for archival purposes. During the guide I copied and converted the SXOS EmuNAND to an Atmopshere EmuNAND. Bringing with it All my saves and my installed games. I have >11.0 Games on the USB drive in Super XCI. That way all the DLC and UPDATES are in the XCI on the HDD as well.. I deleted all installed games and DLC then I shrank down the SX EmuNAND (this breaks installed content in the SXOS EmuNAND anyway but not the saves) . The SXOS EmuNAND is only for save files on my system. 6GB has been enough for me. Mileage may vary. Consider your needs.