The restriction to one idea per note is also the precondition to recombine them freely later. Luhmann wrote notes on A6 paper (4.1 x 5.8 in or 105 x 148 mm). A good rule of thumb for working digitally is: Each note should fit onto the screen and there should be no need of scrolling.
atomicity helps to allow creativity in putting notes together. by having LEGO bricks you can make a lot more than if you only had complete structures.