The biggest issue with not using the webhook is if you are displaying comment numbers for posts on an index page. Loading an index page that displays comment numbers can result in a lot of API calls to Discourse. With the webhook, this problem is completely eliminated. If you are not displaying comment numbers on your site, not using the webhook won’t result in many extra API calls to Discourse.
I’m unsure about why the webhook isn’t working reliably for you. I’m tempted to think the problem is related to Cloudflare. Is there any pattern that you can see for when it works correctly and when it doesn’t?