Heat the olive oil in a large pot over medium heat. Add the onion, fennel bulb and garlic and cook, stirring occasionally, until tender but not browned, 10 to 12 minutes. Stir in the oregano and red pepper flakes and cook, stirring, 30 seconds. Increase the heat to medium high, add the wine and cook until it almost completely evaporates, about 5 minutes. Add the tomatoes and clam juice and simmer, stirring occasionally, until the tomatoes are tender and the broth is slightly thickened, about 15 minutes.
Meanwhile, toss the crab with the lemon zest, 1 tablespoon fennel fronds and a pinch of salt in a medium bowl. Season the flounder with salt and pepper. Place a packed 1/4 cup of the crab mixture about 2 inches from the widest end of each fillet and tightly roll the fish around the crab; insert a toothpick or small skewer through the center to secure.
Gently nestle the flounder rolls in the simmering tomato broth. Cover and cook until opaque, 12 to 15 minutes. Transfer the rolls to a rimmed platter with a slotted spoon and remove the toothpicks; tent with foil and set aside.
Add the cockles to the simmering tomato broth, cover and cook until they just start opening, about 6 minutes. Stir in the shrimp and cook until just opaque and the cockles are completely open, about 2 more minutes. (Discard any unopened cockles.) Transfer the cockles, shrimp and broth to the platter with the flounder rolls and top with the remaining 1 tablespoon fennel fronds.