I always thought that "Khun" was the honorific for Mr. or Mrs. but I noticed on my Covid Certificate they use the honorific "Nay" before my name. Is this just a polite/official form of "Khun"?

นาย /naay/ is more formal than คุณ /khun/ and is only used with men.  (/khun/ is ambisexual.)

 

The female equivalent is นาง /naaŋ/ for married women, and นางสาว /naaŋˑsǎaw/ for unmarried women.

นาย นาง is not more honorific than คุณ

 

while nai appears on official document, if used when addressing the person it is considered condescending. It's only used when a teacher or your mom calls you by your full name, or an official calls you out from a queue at the Amphur or addressed on the envelope when your bill is overdue  

 

คุณ is only afforded when you consider someone you're speaking to to be  of honor, whereas นาย or นาง(สาว) could be any farmer or laborer