Preheat oven to 350 degrees F. Spray a muffin pan with nonstick spray or line with 12 muffin liners.
In a medium bowl, whisk together flour, baking powder, baking soda, kosher salt, cinnamon, nutmeg, and ginger.
In a large bowl, add sugar, melted butter, pumpkin puree, shredded zucchini, eggs, milk, and vanilla extract. Whisk to combine.
Pour the flour mixture into the pumpkin mixture and whisk until just combined. Do not overmix.
Scoop muffin batter into the prepared muffin pan. Fill each one almost to the top.
Place muffins in the oven and bake for 20 to 25 minutes, or until a toothpick inserted in the middle comes out clean with just a few crumbs.
Allow muffins to cool in the pan for 10 minutes, before removing them and placing them on a wire rack to cool completely.
As muffins cool, prepare the glaze: Combine powdered sugar, milk, and vanilla extract in a small bowl. Whisk to combine, until smooth and no longer lumpy.
Spread a light glaze over top of the muffins. Sprinkle the tops with a little cinnamon. Let glaze sit a few minutes to harden before serving and eating.