In the bowl of a stand mixer, combine the all-purpose, whole-wheat, and rye flours with the salt, baking soda, baking powder, 1 teaspoon of cinnamon, and brown sugar. Mix for 10 seconds using the paddle attachment, then add the butter and shortening. Mix on medium speed for 30 seconds.
Combine the honey and vanilla with 1/4 cup cold water in a liquid measuring cup and stir to combine until the honey is mostly dissolved. With the mixer running on medium- low speed, slowly pour the honey mixture into the bowl, giving the mixture time to absorb the liquid. Continue to mix for another 20 seconds, or until the dough comes together. It will still be slightly crumbly. Push the dough into a ball, wrap it in wax paper, and refrigerate for at least 2 hours, and up to 3 days. The dough can be wrapped and frozen at this point.
Take the dough out of the refrigerator about 20 minutes before you are ready to bake. Preheat the oven to 350°F. Cut the dough in half, and lay one half between two sheets of wax or parchment paper dusted with rye flour. Roll the dough as thin as you can get it, ideally 1/8 inch. It will still be slightly crumbly, but just press it back together and keep rolling. Use a pizza wheel, jagger, or knife to cut 2x3-inch rectangles. Use a spatula to separate the rectangles from the wax paper and set them on a lightly greased baking sheet. The crackers won’t spread, so they can be quite close. Re-roll any scraps and repeat—then repeat again with the second half of the dough.
In a small bowl, combine the remaining 1/2 teaspoon cinnamon with the granulated sugar. Sprinkle the crackers with the cinnamon mixture and prick the dough several times with a fork. Bake for 15 to 20 minutes, or until just starting to brown at the edges. Cool on a wire rack. The crackers are great out of the oven, but their flavor and texture improves the next day.
Alana Chernila writes, cooks, sells fresh vegetables, teaches cooking and cheesemaking, and blogs at EatingFromTheGroundUp.com. She is the author of two books, The Homemade Pantry:101 Foods You Can Stop Buying and Start Making, and The Homemade Kitchen: Recipes for Cooking with Pleasure. She lives with her husband and daughters in western Massachusetts.