Removed Atom from Applications. How to remove `atom` command from terminal?
where atomwill result in command not found, true, but because the where command is not found; when using bash. A zsh error would have issued "atom not found"

Try which atom to get the result of /usr/local/bin/atom in bash.

That means you just need to rm /usr/local/bin/atom to get rid of that command.

(Atom.app install also apm, so be sure to remove that as well.)