Toast pecans on a baking sheet at 350 degrees F for 8 to 10 minutes until fragrant. Cool completely.
Grease three 9-inch round cake pans, line with parchment rounds, and grease the parchment.
Whisk flour, sugar, baking soda, cinnamon, nutmeg, and salt in a large bowl.
In a separate bowl, whisk eggs, oil, and vanilla. Add mashed bananas and undrained crushed pineapple. Stir to combine.
Pour wet ingredients into dry. Fold with a spatula until just combined. Do not overmix. Fold in toasted pecans.
Divide batter evenly among the three pans. Bake at 350 degrees F for 25 to 30 minutes until a cake tester comes out clean.
Cool in pans 10 minutes. Transfer to a wire rack and cool completely before frosting.
Beat cream cheese and butter until smooth, 2 to 3 minutes. Add powdered sugar cup by cup on low. Add vanilla and salt. Beat on medium 1 to 2 minutes until thick and spreadable.
Level layers if needed. Frost one layer, stack second, frost, stack third, apply thin crumb coat all over. Refrigerate 20 minutes. Apply final frosting layer.
Press toasted pecan halves into the top of the frosted cake. Remove from refrigerator 30 to 45 minutes before serving. Slice with a sharp knife, wiping blade between cuts.