1. Do we come to an agreement?
2. Do we have a deal?
Are they same things? If not, what are their meanings?
"Do we have a deal?" means exactly the same thing (in every case I can think of) as, "Did we come to an agreement?"
"Do we come to an agreement?" is the (conditional) future tense, but I'll have to think about why that is. Maybe if there is someone out here who is more knowledgeable about transformational grammar than I, he or she can explain.