Questions in English tend to have a different structure than the corresponding statements. The subject-verb order commonly gets reversed ("Are you here?" instead of "You are here."). Often, the question words (who, what, where, why, when, how) get moved to the front if possible as well.
In this case, the question is "How long have you been here for?", put back into standard sentence structure, would be "You have been here for how long?"
The object of "for" is "how long". There is no ellipsis here.
The version if you use "since" would be *"You have been here since how long?" isn't correct. When referring to time, "since" takes a past event or point in time as an object, not a duration. "Since last week", "Since 4 days ago", "Since I went to the store". Not *"Since two days", or *"Since a semester".
In contrast, "for" can have a duration as an object, but not a past event or point in time. "For a week" is fine. "For a week ago" is fine if you are using a different sense of the word "for", to indicate a purpose ("I bought this book for a week ago", meaning that there was something (contextually understood) that happened a week ago that was the purpose of buying the book).
So it would be fine to ask "You have been here since when?", or in inverted structure, "Since when have you been here?" (Note, the "since" moves with the "when", even though the "for" does not move with "how long".)