I don't believe there are any SmarterMail APIs that deal with any message actions once the message is received by a user, beyond something like forwarding the message. There's nothing I could find relating to Mark as Junk, mark for follow up, deleting, marking read/unread, etc. I thought maybe there could be a content filter or event that would work, but nothing there as well. 

Why are you looking to do this? Just kind of curious. (Also, I changed the Thread from a Problem to a Question.)