What did Freud intend as the referent of 'Das Es' (Latin: 'id')? Why didn't he name with the referent?
Short answer
Freud din't come up with that terminology, he borrowed it from his contemporaries. 

Background
According to wikipedia Freud borrowed the term "das Es" from Georg Groddeck, a German physician to whose unconventional ideas Freud was much attracted (Groddeck's translators render the term in English also as "the It").

Nietzsche, who is thought to have influenced Freud also often used the German pronoun das Es. Freud’s English translator indeed used the Latin word 'id'.