I would understand your meaning either way; but 'over lunch' is more idiomatic - you can imagine people talking with plates of food on the table. The other expression sounds awkward to me, but, if you were (for example) at a meeting with a scheduled lunch break, then you might imagine eating (or missing) lunch but continuing the meeting anyway.

The correct choice is "Let's talk about it over lunch." The second sentence is not quite right. Sometimes we choose one English word over without having a standard grammar rule to explain why. I wish I could give you a grammatical explanation that you could apply all the time in situations like this, but this is one of those nuances in English that you'll learn over time. Here are some ways we would use the words over and through in reference to lunch: "Shirley and I talked about the project *over* lunch." (In other words, we discussed the project when we ate lunch together.) "Shirley and I didn't get to talk because we worked *through* our lunch break." (In other words, we were working and didn't get to eat lunch or talk.)