...The key that was hidden on the premises -- is it the one you used to get in that night?
"The key that was hidden on the premises" is the start of a sentence that never gets finished. Then the person comes back and uses a complete sentence with a reference to "key" with the word "it." There is nothing for that first part -- "The key that was hidden on the premises" -- to be or to do in the complete question.
At best, it might be an appositive, but if it is, it is away out of place. An appositive that "precedes" what it renames takes a dash. A sentence that gets started and does not get finished takes a dash.
There has always been a lot of push-back for the dash here. This is my response: If you want a comma, state the rule that covers it. There just isn't a comma rule that works here.
Happy punctuating!
Margie