Well, I am not a developer of atom, but I’d say that is a basic concept of OS X: applications might create files like preferences files etc. which are not removed when an application is uninstalled, but do not harm the system (unlike, for example, entries in the windows registry which should be removed).
Nonetheless, I guess trashing the app, removing
~/Library/Preferences/com.github.atom.plist should take care of the files.
Removing the first one can only be done via the Terminal, just type
rm -r ~/.atom. For the second one you can use the Finder, just use Go -> Go to Folder from the menubar, then type
~/Library/Preferences there and look for the file and delete it.
As for the command-line tools, they are installed manually via the menubar (Atom -> Install Shell Commands). I’d assume there is an uninstall command there, but I haven’t installed them so far so I don’t know for sure.