The thought has crossed my mind too to just disable the reminders for all SSL certificates for all free subdomains.
However, I decided not to do that, mainly because the new situation doesn’t fully cover what the old situation did (mainly regarding subdomains of subdomains). If you were using those, then you must take action. If not, then you do not need to do anything.
The renewal reminder is not perfect for that, but it makes people pay attention to their certificates, so their websites will not break silently.
A different reminder message would be better. But in six weeks from now, all SSL certificates for free subdomains will have expired, by which time the problem will be gone too. So I don’t think it’s appropriate to put a lot of effort into custom messaging.