For the muffins: Place an oven rack in the center of the oven. Preheat the oven to 350 degrees F. Line 24 mini-muffin cups with (1 1/2-inch) paper liners. Set aside.
In a medium bowl, sieve together the flours, salt, baking powder, baking soda, and cinnamon. Add any solids leftover in the sieve to the bowl and mix in.
In a separate medium bowl, whisk together the oil, syrup, and egg. Add the dry ingredients and mix until just combined. Mix in the grated carrot, grated zucchini, and raisins.
Using 2 small spoons, fill the prepared muffin cups 3/4 full with the batter and bake until light golden, about 15 minutes. Cool for 5 minutes. Transfer the muffins to a wire rack to cool completely, about 30 minutes.
For the frosting: In a small bowl, mix together the cream cheese and honey until smooth.
To serve: Spread the cooled muffins with frosting, if using, and serve.