We understand that you are looking to see if Azure Hybrid Connection Manager uses certificate pinning.
Hybrid Connection Manager does not appear to use certificate pinning, which is technology from 2011 and some certificate authorities, such as DigiCert, no longer recommend cert pinning as a best practice.
Hybrid Connection Manager does provide robust security though. Each Hybrid Connection matches to a single host:port combination, helpful for security. It also uses TLS 1.2 for security and Shared Access Signature (SAS) keys for authentication and authorization.
Please let us know if you have further questions or concerns.