Web hooks are not reliable. When engineering your system, you need to implement a scheduled based watcher to go back and clean up hook issues.
I had the REST API e-tag polling working well, but then I discovered my org event stream didn't include label changes. This is a separate thing I needed to poll and at that point I lost my mind. I refuse to keep track of 6+ pieces of state in order to pull essential data from an API.
My current pattern is to list all open issues and then compare their updated_at with persisted copies. If any changes, then I refresh the comments for the issue as well as top-level items (title/body/labels).
Not to mention with Shopify, webhooks are not guaranteed to be at all ordered. You may receive an order.updated event prior to an order.create event. Delivery milage and timing may vary.
So, after all that back and forth we asked ourselves, why do we even bother with webhooks?
Well for one, it helps our clients being real time to improve their shipping speed, keeping real time inventory, and so forth. Secondly, it keeps our processing more flat. We might run an hourly cron to pickup stragglers, but we don't do huge data dumps per hour. In some our busier systems it can be a real challenge when clients do things like monthly invoicing all their customers. Using webhooks and processing records as they come in keeps the queue as small as reasonable.