By default, bundle items are not sold exclusively through bundles.
Merchants may choose to sell bundle items exclusively through bundles for sales & marketing purposes.
To do this: find the product (of the bundle item) in your Shopify store's admin panel.
→ On the right sidebar, find Sales Channels and Apps and click on Manage.
→ Uncheck the Online Store option and click on Done to hide the bundle item on your storefront for sale.
Before unchecking the Online Store option, the bundle item is not hidden:
After unchecking the Online Store option, the bundle item is now hidden: