Preheat oven to 325 degrees. Line 1 dozen regular-size muffin tins or 36 mini muffin tins with paper liners or generously grease with oil or butter. If you want to bake this in a loaf pan, generously grease a 9x5-inch pan well with oil or butter.
Put the grated zucchini in a colander set over the sink and use your hands to squeeze out some of the liquid. Leave in the sink until ready to use.
In a large bowl, beat the eggs with an electric mixer on high until foamy and light yellow, a minute or so. Add the yogurt, canola oil, sugar, and vanilla and beat again on medium until one even color and consistency, another minute. Set aside. You can also do this with a whisk and a little elbow grease.
In a medium bowl, combine the whole-wheat pastry flour, all-purpose flour, cocoa powder, cinnamon, baking soda, and salt. Stir well with a fork to blend all the ingredients.
Add the dry ingredients to the wet and beat on medium just until evenly mixed together, scraping down the sides as needed.
Add the zucchini and chocolate chips to the batter. Mix until just combined.
For full-size cupcakes, fill each tin with a scant Â¼ cup of batter. For mini cupcakes, figure about 1 Â½ tablespoons of batter each (although this can vary depending on the size of your muffin tins).
Put into the oven and bake until a toothpick inserted into the center comes out clean, 25 to 28 minutes for full-size cupcakes, closer to 20 minutes for minis, and about an hour for a loaf.
Remove from oven and leave on the counter until completely cool. Finish with a light dusting of confectioners' sugar, your favorite chocolate frosting, or 1/4 cup of melted chocolate chips (in the case of the loaf).