Preheat the oven to 350°F (175°C) and line a 12-cup muffin tin with paper liners.
In a medium bowl, whisk together the flour, baking powder, baking soda, and salt, then set aside.
In a large mixing bowl, beat the softened butter, granulated sugar, and brown sugar with an electric mixer until light and fluffy, about 2 to 3 minutes.
Beat in the eggs one at a time, followed by the vanilla extract, scraping down the bowl as needed.
Mix in the mashed bananas until fully combined.
Add the dry ingredients to the banana mixture in two additions, alternating with the milk, beginning and ending with the dry ingredients, mixing just until combined.
Fold in the roughly crushed vanilla wafer cookies with a rubber spatula.
Divide the batter evenly among the 12 liners, filling each about two-thirds full.
Bake the cupcakes for 16 to 18 minutes, or until a toothpick inserted into the center comes out clean.
Remove the pan from the oven and let the cupcakes cool in the tin for 5 minutes.
Transfer the cupcakes to a wire rack and let them cool completely, about 25 minutes.
While the cupcakes cool, whisk the instant vanilla pudding mix and 2 cups of cold milk in a medium bowl for 2 minutes, then refrigerate until thickened, about 5 minutes.
In another bowl, beat the heavy cream, powdered sugar, and 1/2 teaspoon vanilla extract to stiff peaks to make whipped cream.
Gently fold half of the whipped cream into the chilled pudding until smooth to create a light banana pudding filling, reserving the remaining whipped cream for topping.
Once cupcakes are completely cool, use a paring knife to cut a small cone from the center of each cupcake and remove it, creating a well.
Spoon or pipe the banana pudding filling into the center of each cupcake, filling the well level with the top.
Fit a piping bag (or zip-top bag with a corner snipped) with a tip if desired and fill it with the remaining whipped cream.
Pipe or dollop the whipped cream over the top of each cupcake.
Garnish each cupcake with a whole vanilla wafer cookie and a banana slice if using.
Chill the cupcakes for at least 20 minutes before serving to help the filling and topping set.