Certain Commands are not Found in Catalina's Zsh
I am going to bypass what could be causing it, to tell you how to “cure” it.

First, find out the exact path of “atom” (not Atom.app).  It is probably embedded somewhere inside of Atom.app, but it's possible the Install Shell Commands copies it to somewhere else.  

If it disappears on a reboot, it might be copied to /tmp (!).  If that is the case, do echo $path and copy it to one of those directories.

After you have atom in a location that won't be erased on reboot, ensure that location is in your zsh $path as discussed in How does zsh find commands?