I don't think they are fused together because of the scene with MX and Terra inside Terranort. If it had fused I doubt they would be separated in that way still. if the fusion theory was correct, the heart would be completely together as one persona not two. And Kairi's heart didnt fuse with Sora's so why would this be different. Also it would be harder to explain that theres a heart with a heart inside one of the two hearts that make the first heart i mentioned up. See? Saying that inside Terranort lies the Heart of Terra and the heart of MX. Within Terra's sleeeps the heart of ME. It makes more sense to the story.
If they fuse, its too confusing. Cuz ur saying they are one yet they are still separate inside of the one heart.