The syntax of second idiom is incomplete as you state it. It is the introductory phrase for a question about some situation or condition ... ... "Why is it that you never call me anymore?" ... "Why is it that time seems to go by faster as I get older? The first and third are almost the same, and could be used interchangeably in many contexts. It can be a response to a statement by someone else ... ... A: I can't really have any sympathy for her situation. ... B: Why is that? ... or a question posed by the speaker himself, seeking an explanation for a statement he has just made ... ... "I just can't sleep on airplanes. Why is that?" It must be noted that the emphasis can be different, depending on the context ... ... Why is that? [all normal -- no urgency or emotion] ... Why IS that?? [the reason is being strongly questioned] .......... "You and I don't seem to talk like we used to. Why IS that?" ... Why is THAT?? [the "that" is something surprising, either positive or negative] .......... A: "I'm not coming to your wedding." .......... B: "And why is THAT??" In the phrase "Why is that so?", the "so" is a bit superfluous. If you google the two phrases using quotes, you'll find this version outnumbered by about 7 to 1. Think of the word "so" as meaning "true"; i.e. Why is that true?" Then it doesn't work well with certain statements ... ... A: "I'm not going to your wedding." ... B: "Why is that so?" ["why is it true that your not going" -- sounds a bit strange]

hi!!i never came across such a structure as in a second variant!!but first and last is ok !the last one sounds more emphatic!!happy new year)

Why is that? and Why is that so? are both the same. They are both used to question why something is the way it is. Example: Your friend tells you that the airplane leaves London on it's way to Hong Kong only at 18:00. You could then question your friend by saying 'Why is that so? or Why is that?