If you are able to send a group email to all or most of the guests, you could send a casual message saying that you've had a great honeymoon.
Then you could tell a little lie and say that when you were sending out the thank you notes, there was one present where the label was missing, and you'd really like to thank the person. So, could the person who hasn't had their thank you note get in touch!!!
And although the email would apparently be to all the guests, you could in fact just send it to the three people by putting their address in the blind copy line.