How are you? Have you tried contacting Zapier Support? Since Zapier is a 3rd party integration they would be the best resource to help you in this case.
But if not, could you tell me a little bit more about these automated emails please? With some more information, I can investigate further for you.
Are the emails Hubspot emails, or is Zapier triggering another system to send emails? If it’s another system, then you might be able to add trackable links or CTAs from Hubspot, but it wouldn’t show up with your Hubspot reporting. Only emails that exist in Hubspot would be trackable by Hubspot.