The bundle "use" statistic is never increased, neither when you put items in or take items out.
- Create a scoreboard objective with "minecraft.used:minecraft.bundle" as its criteria
- Set your score to 0 and show the scoreboard on the sidebar
- Take a bundle and an item
- Add the item in the bundle: the score stays at 0
- Right-click the bundle to take the items out: the score stays at 0
I have added screenshots to demonstrate these steps.
You can also verify in the statistics window that it doesn't increase.