Email to Case Premium is a 100% native Salesforce application and inbound email traffic never passes through Internet Creation's infrastructure. As such, the functionality of the application will not be directly impacted by Transport Layer Security (TLS) encryption protocol changes performed by Salesforce.
Salesforce supports TLS and email relaying provides some additional controls.
For detail, please see Salesforce Knowledge Article #000003756
Email to Case Premium falls under the Email-to-apex category and the article above describes how Salesforce handles security for emails on their platform. Encryption and security in place for email sent using standard Salesforce interfaces will automatically extend to Email to Case Premium.