"What are you doing here?" would be used when you want to inquire why someone is in a place generally. It could refer to literally any place. A house, a store, a park, a country. "What are you doing IN here?" is more specific, and would be used when a person was unexpectedly found in a closed space, like a room. If a man walked into the women's restroom, I would be more likely to say "What are you doing in here?" If I ran into a friend at the store, I would be more likely to say "What are you doing here?"

What are you doing here? = in this place. The place could be a country, a city, a park, a building, etc. What are you doing in here? = inside this place, eg: a room/building. (you should be outside, maybe) 'in' can mean an area: in Brazil, in New York, in the north of the city, or 'here/there'. 'in' can mean 'inside': in the bathroom, in my apartment, in my coffee, or 'in here/ in there' :)

Yes ivan there are one. The word "in" is there