In a medium saucepan over medium-high heat, bring the vinegar, salt, mustard seeds, chile flakes and 3 cups water to a simmer. Cook until the salt has dissolved, about 5 minutes.
Divide the dill, garlic, zucchini and onions evenly between 2 quart-size mason jars.
Pour the hot liquid into the mason jars to cover the ingredients and let cool to room temperature, about 1 hour. Serve immediately or cover with lids and store in the refrigerator for up to a week.