"What did you make?"
作り only means "to cook" if used with food-related terms or if someone is cooking in context, otherwise it'll become "to make, to create, to produce, to build...etc."
何を作りますか？ with no other info will usually mean "what will you make?", but if you ask your friend who is mixing ingredients up in the kitchen, it'll become "what will you cook/make(food)/bake?"
料理 just means "to cook", and you can't 料理 a sculpture or a toy plane.
So when 作り is not paired with any food-related terms, and/or the sentence offers no context that refers to food or cooking, it defaults to the "make, create, build...etc" meaning.
well, the speaker is using the masu form, so I'm guessing that it is needed. You can however just say 何作った？ in casual speech, that's how Japanese people usually speak between friends. I don't recommend skipping particles unless you have experience in the language though, it creates bad habits.
を marks 何 as the direct object, the thing that you did the action of "make" to.
は can't be used because 何 is an unknown; an unknown can't be a topic of conversation.
が marks the do-er or be-er of a verb. This would change the sentence to "What made it", with 何 being the thing that did the action of "make" to something else.