Preheat oven to 450 degrees. Prepare 2 sheets of parchment paper, each 2 feet long.
Place a large lidded skillet over medium heat and add 1 tablespoon of oil. Once oil heats, add the shallots and garlic. Cook until shallots soften, about 2 minutes. Then, add in the clams, wine (or broth) and red pepper flakes. Cover and steam until clams just open, about 3 minutes.
Remove the skillet from the stovetop and discard the garlic. Remove half of the clams from their shells and discard the shells. Season the juice in the pan with salt and pepper, to taste.
Return the skillet to medium heat. Once simmering, add in the zucchini noodles, remaining oil and parsley. Cook, tossing vigorously, until sauce reduces and becomes thicker, about 3 minutes. Season with pepper to taste.
Place a half of the zucchini pasta mixture in the center of each prepared sheet of paper. Drizzle each with some of the pan juices. Then, draw the long ends of the paper over the zucchini pasta so the edges meet. Fold edges over and continue folding to form a tight seal on top of each packet. Repeat with remaining mixture to make another pouch.
Transfer the packets to a baking sheet and bake until paper browns slightly, about 3 minutes. Place the packets on plates and serve with lemon wedges.