Currently, Let's Encrypt indeed has no way of knowing whether a certificate is no longer needed.
In the future, this may become a possible use case for ARI. Clients like certbot could use ARI to set the certificate's replaced status to true when
- expanding or shrinking an existing certificate
- deleting a no longer needed certificate
The ACME server (Let's Encrypt) could then use this information to stop sending renewal reminders for the affected certificates.
Note that Let's Encrypt does not currently implement this functionality (updating cert replacement status), so even if a client would do this, it wouldn't work as of today. But in the future this may become a viable workflow to enhance the renewal mailer.