Honestly, there's so much proof that it's almost impossible NOT to think so. Though I'm hoping the writers do something similar to Speedy from Young Justice... letting the clone flesh out his own personality in a different direction, creating a new character and keeping both Shiros on the team. Even though the hair is awful in my opinion.
Not sure if he's a clone. Maybe the first one is the clone? How long does it take to grow hair that long? How long was he missing the second time? Why did Haggar say that he 'could have been their greatest weapon' at the end of S1 when she was fighting him in the fighter hanger?
Anyone ever seen the movie "Moon" with Sam Rockwell? If you saw it, you'll understand my reference.