There's a subtle difference. You can say "It's cold in here." If you're in a room, a building, a classroom etc. But you can't say it if you're outside. And the same thing applies to "I'm in here." I can say this only if I'm in a room and for an example letting my friend know I'm there. I can't say "I'm in here" if I'm waiting to meet with the same friend at the town square and trying to make them recognize me by shouting. Same applies to every example in fact. "Why are you here?" "Why are you in here?" "It's dark here." "It's dark in here." and so on.

"Here" indicates a specific location of a person or thing at a particular moment. If you add "in" and say "in here," it would imply a location inside a given place; such as a room, building, car, etc. Simply saying "here" does not give any evidence about what kind of place is being referred to, but if hear "in here," you can at least infer that there is a "container" or sorts toward which "in" refers to. I hope this helps. If you are still confused, I'll try to explain it in another way.