"Why are you here now" would in my view correspond best to: "Why have you come here (now)?" Your perspective is the present (perhaps either because you and/or the other arrived recently), and you want an answer for a present purpose. "Why did you come here?" implies a finished time in the past, perhaps some time ago. Your interest may be more in the reason for coming at that past time. If you added the word "now" it would sound a bit funny to me, as a UK speaker. However, US speakers sometimes choose the past simple instead of the present perfect in informal contexts. In practice, in most contexts, this option and the present perfect option would be interchangeable. "Why do you come here?" implies a frequency e.g. sometimes, every week, every time you are in trouble. It would be correct only in this context.

1 is the closest one to "why are you here?" ..and your understanding of the meaning is right. As for 2, it makes sense and is not wrong, but it doesn't have the exact meaning of "why are you here?" Instead, the question fits in a situation where you ask a person why they go to a certain place often.

why do you come here? => What do .........