This phrase is very literal in origin. Peas in a pod are identical, you can't really tell one from another. Figuratively we use it to mean two things, or people, are as close to identical as they can get. 

Goody Two-Shoes is a poor orphan named Margery Meanwell who only has one shoe. When she's given two shoes she is so happy she tells everyone she meets. Her story is found in the 1765 nursery tale The History of Little Goody Two-Shoes. Read here about how goody got added to her name.  These days the phrase means that the person being called a "goody two shoes" is smug and above virtuous. 

Israel Zangwill wrote a century ago that “Life is Janus-faced, and the humorist invests his characters with a double mask; they stand for comedy as well as for tragedy.” Janus, a Roman God, has the image of a man with two faces, looking forwards and backwards. Read more about him here .  It seems obvious what the phrase means when used today. A person is portraying two distinct personalities, at least one of them deceitful. In case you weren't sure, it's not a compliment.