Q1) According to that, the meaning of #1 and #2 are the same, aren't they?-- Yes.
Q2) #1 is the normal construction than #2 considering 'John' and its pronoun in the later cluase, isn't it?-- 'Normal'? In spoken English, perhaps.
Q3) When and Why the structure of #2 is used?-- It is a style technique; it depends on how it fits into surrounding text.