Your problem is probably related to a specific package / s, which takes a lot of your processing. I recently had a problem when an atom froze / lagged every 20-30. I would type the text and it just freezes, and then after about 5-10 seconds, each letter that I clicked will appear. I ended up basically trying a few different things and ended up eliminating my problem.
I started by trying to run:
atom --safe
This command starts an atom without community packages. It is used to troubleshoot if your problem is a community package or an atom package. When working in safe mode, find out if your problem persists. If so, this is not a community package.
After I excluded community packages, I basically went through Atom packages, trying to narrow down the source of my problem. I would disable 10-20 packages at a time, and then try to reproduce my problem. Having done this 3-4 times, my question has stopped. In the end, I found a package with errors and was able to disable it. My question immediately ended.
Atom Debugging Guide: https://flight-manual.atom.io/hacking-atom/sections/debugging/
Note: Make sure the atom is updated with the latest secure build. You can also try to completely remove the atom from your computer, and then reinstall it.
Note: You must also consider that this may be your machine. I recently upgraded from my MacBook Pro to the Samsung Evo 850 SDD. I tried to develop a responsive application, and the simulator was very slow when I could not do anything. Upgrading the hard drive resolves this issue. (Also, the atom has been much faster since the update.)