I am Unable to Uninstall an Applications like Node or Atom in OS X
Have you tried emptying your trash? Spotlight can find and open (IIRC) applications that remain in trash.

If after your trash is emptied and you still see Atom or Node, try, in Terminal:

sudo find / -iname 'thing'


in which you should substitute thing with your search query.

EDIT: in Spotlight, when you hold Command, does it show a path at the bottom of the spotlight window?

EDIT 2: As per @Lizzan's comment, do check your Downloads, Documents, and any other user-related folders.