Generally the only time you would use "had" is if the other person's current status is unknown. Have you two spoken lately would be asked by someone who knows, or believe they know, the status of the other person. A detective who is working on a murder case, or a missing persons case, may use "had you two spoken lately?" if they know the person is no longer living or able to talk. They may, however, use "have" as well. In short, have you two spoken lately would be used where both people are known or believed to still be in contact with each other, whereas had you spoken implies that person isn't able to speak for some reason. It's a good question but I'm finding it somewhat hard to be succinct in an answer. Does that help at all?

Have you two spoken lately? Person A is asking person B if person B and C have spoken recently, using today as a reference point. Meaning, have you two spoken in the last few days, last few weeks, etc. Had you two spoken lately? This is not correct English, but here's how something close would work. Suppose person A is talking to person B and they're talking about an event that occurred one year ago. Person A wants to know if, some short time before that event, person B spoke to person C. Person A might ask: Had you two spoken in the days before the event? Had you two spoken in the weeks before the event? etc. I don't think you can say "Had you two spoken recently." Because the "recently" refers to a "recently before now" and the event being discussed is not now but some time ago.