I think in that context "victims" is an adjective, or it needs a preposition instead "Where they THE victims?" (victims is now a substantive) or instead "where they victims?" I understand victims is now an adjective, therefore "ĉu ili estis viktimaj?" should be the right answer.
No, you would say "were they the victims?" if they were all of the victims. If they are some of the victims, but not all of them, you say "were they victims?" And in that sentence, "victims" is definitely a noun. (Native speaker of English, New England variety.)