Tense – What Will You Have for Lunch or What Do You Have for Lunch?

Both alternatives are correct as pictured in this ngram chart, but I, personally, would prefer the simple present as the use refers to scheduled events in the near future.

These distinctions are simply guidelines but not hard-and-fast rules. The shift of tense does not indicate that the event has not taken place.

Let's say that she agreed last week to have lunch with Susan today, to discuss a business proposition. The lunch does take place. She has a sandwich. Susan has soup. If the question is about what she said, it doesn't matter whether the lunch took place or not:

When I spoke with her on the phone, she said she would have lunch with Susan today, and they did indeed have lunch. She's a woman of her word.

Not needing to change the tense when the assertion is still true does not imply the corollary that changing the tense means the assertion is now false:

He said his brother worked in Milan.

His brother may still work in Milan. The shift of tense signals that the speaker is reporting the speech of another, not making the assertion himself.