Preheat oven to 350 degrees F (175 degrees C). Line 2 muffin tins with cupcake liners.
Place 1 vanilla wafer flat-side down in the bottom of each cupcake liner.
Blend vanilla cake mix, water, eggs, and vegetable oil in a large bowl with an electric mixer on low speed until moistened, about 30 seconds. Beat at medium speed until smooth, about 2 minutes. Fold in mashed bananas and 1 cup crushed wafers. Scoop batter into prepared tins.
Bake in the preheated oven until a toothpick inserted into the center comes out clean, 18 to 20 minutes. Transfer cupcakes to a wire rack to cool, about 30 minutes.
Combine vanilla pudding and sliced banana in a small bowl.
Scoop out tops of cooled cupcakes, leaving a small hole in the middle of each. Fill holes with pudding mixture. Place a heaping spoonful of whipped cream on each cupcake; garnish with remaining 2/3 cup crushed vanilla wafers.