If the INBOX or any other folder is shown in the Smart folder, the same account's Sent messages will also be shown. You probably have another folder in that account set to "Sync as Plain" and the "Show in Smart Folder" is enabled.
Ok, after a long time, I'm still not able to sort this issue out.
There is an IMAP account that has the Inbox folder set as
Synchronization: Synchronize folders
[x] Use Push Mail
[ ] Show in Smartbox
[ ] No Notifications
[x] Color id...
The Sent folder is set to
Synchronization: Sync with Sent
[ ] Use Push Mail
[x] Color id...
That IMAP account I like to hide in the smartbox. Inbox is hidden, but the Sent mails are still shown. What did you mean with sync as plain? I don't have a
[ ] Show in Smartbox option for the Sent folder