Prepare bacon.
Preheat oven to 350 degrees F. Spray whoopie pie pans with cooking spray. If using a regular baking sheet, line with parchment paper and see notes at the end of the recipe.
In a medium sized bowl, combine flour, baking powder and baking soda. Make sure it is combined well. Sifting it together is also a great idea.
In the bowl of a stand mixer, combine butter and suger until light and fluffy; about 2 minutes. Add eggs one at a time and add banana extract. Scrape down the sides of the bowl. Add bananas and mix until fully incorporated. Turn mixer to low and add flour mixture. Mix until combined. Fold in bacon and 3/4 cup chocolate chips.
Using a 1-3/4" scoop, scoop cookie dough into each well of the whoopie pie pan. Press extra chocolate chips on top (these will not sink in and make the cookie look beautiful) about five. Bake for 12-14 minutes or until edges are barely brown. (Make sure to always begin baking with a cold cookie pan.)
Remove from the oven and transfer immediately to a cooling rack.
When cookies are completely cool, combine all ingredients for the glaze in a small bowl. Mixture should be very thick, but pourable with a spoon. Glaze each cookie in a zigzag design, sprinkling sea salt on top before the glaze drys.
Note: If you are NOT using whoopie pie pans to make these cookies, I would suggest refrigerating the cookie dough until it very cold. This will help it from spreading flat while baking.