if you plan on using emuMMC then you will need to enable it.
if you don't plan on using emuMMC then you can keep it disabled.
if you don't know what emuMMC is
The emuMMC (or EmuNAND) refers to the copy of Switch’s internal storage, which is saved on SD card. The copy includes all the content that is required for running Switch, including firmware, data storage, system settings and games that are installed to internal storage.
Therefore, you can have multiple separate installations of Switch’s operating system. Besides, any changes made to an emuMMC like WiFi settings, installed games will not affect other emuMMCs or sysMMC.