Heat 3 tablespoons of the oil in a medium saucepan over medium-high heat. Add the onion and cook until soft. Add the garlic and cook for 30 seconds. Add the rice and stir to coat with the mixture; cook for 1 minute. Add 3 cups water, tomatoes, season with salt and pepper, and bring to a boil. Reduce the heat to low, cover the pot, and cook until the rice is tender and the water is completely absorbed, about 14 to 16 minutes. Remove from the heat and let sit 5 minutes. Fluff with a fork and stir in the mint and parsley. Let cool.
Stuff the squid with the rice mixture. Drizzle half of the remaining oil in a medium baking dish. Add the squid and drizzle with remaining oil and the tomato juice and season with salt and pepper. Bake until the squid is tender, about 25 to 30 minutes. Serve immediately.