The purpose of marking email as Not Junk is so that Mail can learn not to flag it. However, Mail may not be flagging it, so it is not actually marked as junk. Since Mail doesn't think it is Junk, there is no purpose in marking it Not Junk from within Mail.
Spam can be moved into the Junk folder in various ways.
1) Your email provider (iCloud, Gmail, etc) can move it to the server Spam folder before it is ever delivered to you.
2) Your email provider or anyone else that touches the email while it is enroute to you you can mark the email with Spam headers. If you have the Junk Mail filter set to Trust Junk email headers, Mail will move the message to the Junk folder, but won't mark it as Junk because it has no idea why somebody else marked it as Junk.
3) Mail identifies the email as Junk and moves it into the Junk folder and also marks it as Junk
If 1) or 2) applies, the message is not marked as Junk because Mail does not know why.
You can only mark it as Not Junk if 3) applies.
For 1) and 2) you must log into your email provider's web portal and tell it that the message is not Junk so that it can learn to not mark it as Junk in the future.