I translated this as, "No, it is at school." How would we know from the Czech version that this refers to a boy rather than a thing. Would it be wrong (in Czech) to answer the question, "Is your book in the car?" as follows: "Ne, je ve škole" (i.e., "No, it's at school.")
Yes, for the question "Is your book in the car?" you can use the answer "Ne, je ve škole" ("No, it's at school."). The same you can use: "Is Katerina at home?" ("Je Kateřina doma?") "No, she is at school" (Ne, je ve škole"). In alone Czech sentence ("Ne, je ve škole") you cannot identify if it refers to a boy or a thing. You have to say "Ne, ona je ve škole" but more frequent answer is without "ona".