Learn Hardcore Indonesian: Kamu di mana?

Yes. Both Kamu di mana? and Di mana kamu? are natural. Putting di mana at the end is very common in everyday speech; putting it first can sound a bit more formal or put focus on the location. A very formal variant is Di mana kamu berada?

Why is there no verb like “are” in this sentence?

Indonesian usually doesn’t use a verb like “to be” in sentences about location. The preposition di (“at/in/on”) links the subject to the place, so Kamu di mana? is literally “You at where?”

What does di mean here, and how is it different from the prefix di-?

Here di is a preposition meaning “at/in/on” and is written as a separate word: di rumah, di Jakarta, di kantor.
The prefix di- marks passive verbs and is attached to the verb: ditulis (written), dibuat (made).
Rule of thumb: preposition di is separate; prefix di- is attached.

Is it di mana or dimana?

Standard Indonesian spells it as two words: di mana. You’ll see dimana in casual texting, but avoid it in formal writing. Many style guides (including KBBI-based guidance) insist on the two-word form for the “where” question.