I'm not a native Danish speaker and I certainly do not know the language well enough to answer your question. But I do believe that vagueness and ambiguity are part of all languages. So I wouldn't be entirely surprised if the answer to your question was "Hvad spiser hvalerne?"

Of course, as with any potential ambiguous utterance, you may, as a listener, have to ask for clarification. Or as a speaker you may clarify what you are saying by giving more information to the listener (e.g. "Hvad dyr spiser hvalerne?" ("What animals are eating the whales?"

Unamigously, you could say something like "Hvad er det, der spiser hvalerne?" or "Hvilket dyr er det, der spiser hvalerne?".