When you uninstall a custom app in Shopify, the webhooks created by that app are removed. However, Metafields/MetaObjects persist even after the app is uninstalled.

If you reinstall the app, the webhooks are recreated, and the old Metafields/MetaObjects remain accessible to the shop. However, if the shop tries to create new Metafields/MetaObjects with the same name, an error will throw.

Additionally, if those Metafields/MetaObjects are owned by the shop, they will be removed upon uninstallation.