Welcome!
Unfortunately, you can only import all notes at once. This is because of how Apple Notes is designed. I don’t know the technical details well enough to explain it, but it is a very closed system without any proper files. See here if you’re interested to learn more:
… So I don’t even know if you can consider DEVONthink’s import “native”. But it does work surprisingly well.
You could use a Smart Rule to filter duplicates like suggested here: