Who in the clause who you were is not the object of you. Only transitive verbs can have an object; and the verb to be is not transitive. It is a copula verb that "links the subject to a subject-related predicative complement†". For this reason who is correct in the sentence: Nobody had any idea who you were.
†The definition of copula in the Oxford Dictionary of English Grammar, p102.
"It's me/I they want!"
You may be confused because of the existence of sentences like the following:
"I am [whom they want]."
Here, the subject is "I." The complement is the relative phrase "whom they want." The relative pronoun "whom" is prescribed in this context because it is the object of the relative clause.
The sentence you're asking about has a different structure:
"It's me/I [they want]!"
This sentence is definitely not equivalent in structure to "They want me," so just because "me" is the object of that sentence doesn't mean it's an object in your sentence. I actually don't remember if "it" or "me/I" is considered the subject in sentences like this (I'd guess "it" because the verb agrees with it), but it doesn't make a difference for your question because the main verb is "to be". Prescriptively, the complement of the verb "to be" is supposed to have the same case as the subject, which in this case would be the nominative.
Unlike "whom," "I" and "me" are personal pronouns, not relative pronouns, so it's not possible for "me/I they want" to constitute a clause.
Since "me/I is not part of the embedded clause, the case of the pronoun is just determined by its role in the matrix clause (similar to your example "It is I whom they want" or the situations discussed in the following questions: Which is grammatically correct: "Let he who..." or "Let him who...", Is it acceptable to start an emphatic sentence with "It is he who…"?).
So the prescribed form would be “It's I they want!”
But "It's me they want" sounds grammatical to me, and I'm pretty sure to many other English speakers, so that's also OK (see Which one is correct to say: "It's me" or "It's I"?).
Interestingly, though, "It's I" is still more common than "It's me" when followed by a relative clause starting with the subject pronoun "who," according to Barrie England's answer to the following question: It is I who am at fault? Possibly, the reason is because many people find sentences with first-person verb agreement but not "I" (such as "Remember me, who am your friend”) jarring.
“Who is it you asked?”
This is just the question corresponding to the statement "It is __ you asked." When you form a question, the prescriptive rule is that the interrogative pronoun takes the same case as the corresponding word in the equivalent statement. (In normal speech in real life, the situation is more complicated since we can say "It's me" but not "Whom is it?")
Since we established that the pronoun in "It is me/I you asked" is not a grammatical object, we would use "who" and not "whom."
Best Answer
In this example, it should definitely be who.
A single word question like that is typically seen, grammatically, as an ellipsis for a full-sentence version, as you say. But elided words/phrases are almost always things which have already just been said, so following “He ate the entire cake,” the natural ellipsis would be “Who [ate the entire cake]?”, not “Whom [are you talking about]?”.
Even in cases where it would make formal sense, though, “Whom?” is rarely used alone:
“Whom did the tiger eat?” or “Ate whom?” sound fine to my ear (as do their equivalents with “who”), but “Whom?” alone sounds quite stiltedly pedantic. As ShreevatsaR has described very well, whom is — while not obsolete yet — certainly of limited use, and when in doubt, who is pretty much always an acceptable alternative nowadays, and is often more idiomatic.