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I know little about s/mime encryption. But why do we need to decrypt old emails with the same protocol? In my head, I imagine certs would be for transport, and your server or host should handle encryption at rest no? So short lived transport certs, and whatever storage encryption you want. What am I missing here?

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S/MIME is about the mail (content) itself, not the transport. For the transport part there are things like (START)TLS and MTA-STS. With S/MIME you include your certificate in the mail and can either sign the mail with a signature (with your private key, others can verify it using your public key from the certificate) or encrypt the mail (with the receiver's public key, so only he can decrypt it using his private key). Certificate trust is determined normally via the CA chain and trusted CAs.

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