It means "Dwarf." Joaquin Guzman is short and, therefore, referred to as "El Chapo."
Sep 09, 2008 Rating
El Chapo in English by: Clint Tustison
From what I understand, the term "chapo" comes from the word "chaparrito", which means very short in Mexican Spanish.
So taking it from there, I would say that El Chapo is equivalent to something like Shorty or Short Stuff. But I think it is only used in Mexican Spanish. I don't think it's used in Central or South America.