Preheat oven to 350 degrees F (175 degrees C).

Combine 3/4 cup water, achiote paste, onion, juice of 2 limes, juice of 1 orange, vinegar, garlic, 1 teaspoon oregano, salt, and pepper in a blender; blend until smooth.

Season both sides of the fish fillets with salt and pepper, then brush the top with melted butter. Arrange fish fillets in a baking dish. Add shrimp on top and cover with achiote sauce. Cover baking dish with aluminum foil.

Bake in the preheated oven until fish flakes easily with a fork, about 30 minutes.

Place red onion and habanero peppers in a glass bowl. Add 1 cup water, juice of 1/2 orange, and juice of 1 lime; stir well and season with salt, peppercorns, and Mexican oregano.

Serve fish and shrimp with achiote sauce and top with habanero sauce.