Preheat oven to 350 degrees. Whisk flours, wheat germ, salt, baking soda, and cinnamon in a medium bowl; set aside.
Put butter, brown sugar, and honey into the bowl of an electric mixer fitted with the paddle attachment; mix on medium speed until pale and fluffy, 2 to 3 minutes, scraping down sides of bowl as needed. Reduce speed to low. Add the flour mixture, and mix until combined. Mix in chocolate chips.
Turn out dough onto a floured surface, and divide into quarters. Roll out each piece between 2 sheets of floured parchment paper into rectangles a bit larger than 9 by 6 inches, about 1/8 inch thick.
Using a fluted pastry wheel, trim the outermost edges of each rectangle, and divide into equal-sized squares. Stack parchment and dough on a baking sheet and chill in freezer until firm, about 20 minutes.
Remove two sheets of dough from freezer. Pierce crackers using the tines of a fork. Transfer to large baking sheets lined with parchment paper. Bake, rotating halfway through, until dark golden brown, 8 to 9 minutes. Repeat with remaining dough. Let cool on sheet 5 minutes; transfer crackers to wire racks to cool completely.