Files emunand are a little slower than partition emunand because files emunand use one more virtualisation process than emunand via partition (I will not enter in details cause I don't have the skills to explain this correctly but it's something that I have already discussed with
@eliboa); but the difference is not realy perceptible in practice.
Emunand via partition is realy better on an SD witch use EXFAT file system because with this configuration files emunand could corrupt itself, thanks of the EXFAT driver of the OS of the Switch. And like you say partition emunand is also better in case of a problem on the main partition, at least you don't loose your game saves.
To copy the partition emunand you can use NXNandManager or the Nand Toolbox of my Ultimate-Switch-Hack-Script, Emutool can also do the job.