What does que onda mean?

The answer depends on context, spelling and punctuation.

The Word que can mean what or that and sometimes how.

The Word onda means wave (as in radio waves)

The Word Honda/o (sounds the same as onda) means deep.

So the question ¿Qué onda? could be "what wavelength?" (poor grammar, but still sometimes used. Which is the wavelength (¿Quál es la onda?) is the preferred way to ask that question.)

The statement "Que honda," could means "how deep". A comment made to a girl or woman who made a profound statement.