In macOS Mojave v10.14.x, Apple disabled subpixel antialiasing on all monitors by default. Previous to Mojave, subpixel antialiasing was disabled only on Retina displays or on all displays if the "LCD font smoothing" option was disabled in System Preferences. With this change in Mojave, some users have reported that their fonts in Atom appear "thinner" or "dimmer" than they did previously. It can look better or worse depending on your font and theme selections, but in all cases this is completely a side-effect of the change that Apple made to their font rendering and is outside Atom's and Electron's control.
If this change is something that you dislike, there are a couple workarounds that the community has identified.
defaults write -g CGFontRenderingFontSmoothingDisabled -bool NO
This appears to re-enable the old "LCD font smoothing" option that was removed in Mojave. It is important to note that this is an OS-wide change.
Add the following to your stylesheet:
This has the benefit of being a change local to Atom only if the rest of the OS looks fine to you.