Do I need to keep a 64-bit version number secret?
For most purposes, you probably don't need to provide confidentiality protection for the version field.

There may be some settings where the version field allow traffic analysis, and to analyze that, we'd need to know so much detailed information about your particular protocol that the question would probably become too localized to be a good fit for this site -- but for most circumstances, you don't need to worry about confidentiality protection.

I do recommend you do apply integrity protection (e.g., the MAC, as shown in your question).  The word "protect", in cryptography, is ambiguous, and it's important to understand that confidentiality protection is not the same as integrity protection.