The API deprecation message is simply a warning that the API version you are currently using will be deprecated soon. You need to update to the latest API version (2023-07 at the time of this message) to eliminate this warning. To execute this update, navigate to your app setup configuration on partners.shopify.com. Additionally, ensure that your code is using the latest API version.
Regarding the proper registration of webhooks, I recommend updating to the most recent version of the Shopify API and following the webhooks guide available on their GitHub repository. Here is the repository link: https://github.com/Shopify/shopify-api-js