Preheat oven to 325ºF and line a large baking sheet with parchment paper. Whisk together the flax meal and water in a small bowl to make your flax “egg”, and set aside.
In a sauce pan over low heat, whisk together the maple syrup, coconut oil, and coconut sugar. Continue whisking until the sugar melts and the mixture becomes smooth, about 4-5 minutes. Transfer to a large mixing bowl, and whisk another minute to integrate the coconut oil. Whisk in the flax “egg” mixture, the cocoa powder, vanilla extract, salt, cinnamon, cayenne, and smoked paprika, just until smooth. Switch to a silicone spatula or wooden spoon, and mix in the all-purpose flour. Stir in the chopped chocolate chunks and cacao nibs.
Cover mixture with plastic wrap and refrigerate for 10 minutes. Once chilled, remove from fridge and scoop cookies out in 2-3 tablespoon scoops and flatten to ½" disks. Bake for 18 minutes, then cool on a wire rack.
While cooling, melt ½ cup chocolate chunks in a double boiler or microwave and mix in 1/8 teaspoon smoked paprika. In a small bowl, mix together the pepitas, cacao nibs, and flaky sea salt. Once cookies are cool, drizzle with melted chocolate, sprinkle with the pepita and cacao mix, and finish with a pinch of smoked paprika.
Serve immediately, then store in an airtight container for up to a few days.