Preheat oven to 450 degrees. In a 9-by-13-inch baking dish, toss together leeks, lemon juice, oil, lemon zest, thyme, 1/2 teaspoon salt, and 1/4 teaspoon pepper. Cover with foil, and bake until leeks just begin to soften, 8 to 10 minutes.
Remove baking dish from oven. Add tomatoes, and toss to combine. Season both sides of cod fillets with 1/2 teaspoon salt and 1/4 teaspoon pepper; place on top of vegetables.
Cover dish and bake until fish is opaque throughout, about 15 to 20 minutes. Serve immediately.
Cut away and discard the root and dark-green leaves of the leeks, then thinly slice the white and light-green parts crosswise into rounds. Wash the pieces in several changes of cold water until there's no more grit at the bottom of the bowl. Drain on paper towels.