Whisk together flours, wheat germ, cinnamon, baking soda, and salt in a medium bowl. Cream butter and brown sugar with a mixer on medium speed until pale and fluffy, about 2 minutes. Beat in honey. Scrape down sides of bowl. Add flour mixture, and beat until combined.
Turn out dough, and divide in four. Shape into flat rectangles, and wrap each in plastic wrap. Refrigerate until firm, about 20 minutes. Working with one piece at a time, roll dough to 1/8-inch thickness on a lightly floured sheet of parchment paper laid on the work surface.
Line four rimmed baking sheets with parchment. Using a pastry cutter, cut dough into 1 1/2-by-2 1/2-inch rectangles. Transfer to prepared baking sheets. Place baking sheets in the refrigerator until dough is firm again, about 30 minutes. While dough is chilling, preheat oven to 350 degrees.
Bake crackers until golden brown, 13 to 15 minutes. Let cool briefly on baking sheets, then transfer to a wire rack and let cool completely. While crackers are cooling, make filling.
To assemble, spread 1 1/2 teaspoons of filling on the underside of one cracker. Sandwich filling with another cracker. If desired, drizzle assembled cookie sandwiches with chocolate, and refrigerate until set.
Finished sandwiches can be refrigerated in an airtight container for up to 2 days.