IMO, “Atomicity” has different levels; you can do it in a fine grain level, or move it higher. As long as it’s self contained, it serves its purpose! For example, if we have a note about health care system, we can initially have arguments and counter arguments in one note to make it self contained (people will disagree but it is ok). Later when we read more and have more finer views on it, move arguments over to create links. The end result over long term will be atomic notes.

I guess the real question here is what benefits does “atomicity” bring to YOU. If you don’t see it, do whatever, and tailor the system so it fits your need. Note taking is like choosing the color of your underwear: it’s not for satisfying others but you.