I have built boats both ways, and both have advantages and disadvantages. My first boat was bead and cove, and because of cost issues, I went with planed edges on the second boat. The second boat went together nicely, and I was able to achieve nice tight joints. It did take a while to put the boat together, however.

I think ideally I would use bead and cove on the hull, and simply plane the edges on the deck where the patterns are more complex, to avoid the problems you write about.

Good luck.