Joker probably knows but keeps it to himself. He enjoys messing with Batman. If he accidentally let it slip that Batman was Bruce Wayne others would terrorize or destroy Bruce and his loved ones. Joker wants to keep Batman to himself. If that makes any sense.
I don't see the big deal with this issue. The issue was kind of boring really and the kiss wasn't even that romantic or epic. It was more like a teenager movie kiss where they are sitting on the roof of the garage.