I tried Atom today (the prebuilt .deb of 0.207.0) on my MacBook Retina running Debian Linux, and there seemed to be no HiDPI support. The main text is too small; the menu text is OK, but it doesn’t quite fit vertically in the menu bar.
I found some old posts etc on the subject, but most were quite old, saying it wasn’t supported yet and you have to enter all the font sizes manually. But some said it should work automatically when Chromium supports it. The full Chromium browser does support HiDPI now, but not in this Atom package. Was it built with HiDPI disabled?