Preheat the oven to 325 degrees F. Prepare a mini muffin tin with paper liners.
In a large mixing bowl, add the all-purpose flour, whole wheat flour, wheat germ, brown sugar, baking soda, baking powder, cinnamon, and 1/4 teaspoon salt. Whisk well to combine, making sure there are no lumps in the mixture.
In a separate bowl, add the zucchini, eggs, milk, applesauce, canola oil, and vanilla. Whisk well to combine, making sure that the eggs are incorporated properly.
Pour the wet ingredients into the dry ingredients and mix until just combined, taking care not to overmix. Place the batter into the prepared muffin tins, filling them to the brim of the liner, about 1 tablespoon. Place into the oven and bake until a toothpick inserted into the middle of a muffin comes out clean, about 15 minutes.
For the glaze:
Meanwhile, in a small bowl, mix the cream cheese, orange zest, orange juice, and maple syrup.
Remove the muffins from the oven and cool on a wire rack for 15 minutes. When ready to glaze the muffins, dip the tops of them, 1 by 1, into the glaze, turning the muffin in a circle to coat the top evenly. Serve, or store in an airtight container for up to a week. Alternatively, prior to glazing, freeze for up to 1 month.