Preheat the oven to 350°F (175°C) and line a muffin tin with paper liners or grease it with cooking spray.
In a large mixing bowl, whisk together the all-purpose flour, whole wheat flour, baking soda, baking powder, cinnamon, nutmeg, and salt until well combined.
In a separate bowl, beat the eggs, then add the vegetable oil, honey (or maple syrup), and vanilla extract. Mix until well combined.
Fold the grated carrots and zucchini into the wet ingredients.
Gradually add the dry ingredients to the wet mixture, stirring gently until just combined. Do not overmix. Fold in the chopped walnuts and raisins if using.
Divide the batter evenly among the muffin cups, filling each about two-thirds full.
Bake in the preheated oven for 20 minutes, or until a toothpick inserted in the center comes out clean.
Remove from the oven and let cool in the tin for about 5 minutes before transferring to a wire rack to cool completely.