Verb agreement with "who" in a question

Reference is not everything. Who in a question (as opposed to a relative clause) can be and usually is singular in reference, but its reference is indefinite -- that's the point of Wh-questions, after all.

It's also worth noting that be is the only verb that distinguishes singular and plural in the past tense. With any other verb but be the form would be fixed, and number agreement would never occur.

The upshot is that, since one need not know (and is conventionally assumed not to know) the answer to one's question, interrogative who, what, and which subjects can be assumed to agree with singular verbs in the question. Even if you know better, it's simpler to avoid the complication.

Interrogative pronouns are not really referential -- like all the small words, articles, prepositions, auxiliaries, particles, and so on, they're part of the grammatical machinery, and they don't carry meaning so much as (attempt to) shore up the structure.

Think of them as being officially singular, like clauses and phrases as subjects:

• Down the toilet is/*are where they go.
• That they left early was/*were lucky for you.

we use the singular verb with "who", but that doesn't always make sense.

I know it's normal to say, "Who were they?" and not "Who was they?" as well.

It is true in general that “we use the singular verb with ‘who’” in questions, but “with who” doesn’t mean it applies to any sentence containing “who”. Because verb agreement in English is always based on the subject of a clause, what this rule really means is that we use a singular verb in a clause where the interrogative pronoun who is the subject.

In sentences like “Who were they?” or “Who are they?”, “who” is not the subject, so that rule doesn’t apply. “They” is the subject, so “were” and “are” are used in agreement, just like “am” is used in agreement with “I” in “Who am I?” “Who” comes at the start of the sentence despite not being the subject because it is a wh-word, like where in “Where were they?”