Learn Croatian: Gdje je ključ?

je (is) is a short "clitic" word, which means it doesn't have its own stress and needs to lean on the word before it. In Croatian, these short words almost always want to be in the exact second position in a sentence. Since Gdje takes the first spot, je naturally locks into the second spot.

Why don't we use li to ask this question, like in Je li to ključ?

You only use li when you are asking a "yes or no" question (like "Is that a key?"). When you use a specific question word like Gdje (where), Tko (who), or Što (what), you don't need li. You just put your question word first, followed immediately by the short verb.

Can I also use Gdje to ask "where" someone is going to put the key?

No, Gdje is specifically used to ask about a static location—where something is right now. Because we are just asking where the key is currently located, Gdje is the right word. If you want to ask about a destination (where something is moving to), Croatian uses a different word (Kamo).

Does the word ključ need a special ending here?

No, it stays exactly as it appears in the dictionary. In this sentence, the key is the main subject—it is the thing performing the action of "being" somewhere. Subjects always stay in their basic, unaltered form (the nominative case).