In a small bowl, combine the soy sauce, water, fish sauce, and sugar; set aside. Heat the oil in a large non-stick skillet over medium-high heat. Add the garlic, ginger, and chile flakes, and cook until fragrant, about 30 seconds. Add the shrimp and stir-fry until pink but still translucent in the middle, about 2 minutes. Transfer the shrimp to a medium bowl with a slotted spoon. Add the onion, pepper, and chile to the skillet, and stir-fry until lightly browned, about 2 minutes. Return the shrimp to the pan along with the soy sauce mixture. Bring to a boil, and stir-fry until the sauce glazes the shrimp, about 1 minute more. Add the tomatoes and stir until coated with sauce, about 15 seconds. Remove pan from the heat, stir in the basil, mint, and lime juice. Transfer to a serving dish, serve immediately.