Atom has a problem in dealing with Devanagari, in that the cursor position does not always reflect the actual position if there is some Devanagari text in the current line. Same goes for selecting within lines containing Devanagari.
I can also see that Atom renders Devangari as fully formed Devangari with half-forms, conjuncts (ligatures), and so on. For an editor I would much prefer the Sublime Text approach, where Devanagari text is treated as a string of characters with no attempt to render half-forms, conjuncts, and do the other advanced OpenType compositing features. Instead the text is rendered the way it is typed, which is much much easier to edit.