Yes it is possible. See our changelog here: https://boxcryptor.desk.com/customer/portal/articles/1188696-boxcryptor-2-0-for-windows-changelog)
Added: When creating a file or folder in a plain text folder a dialog pops up asking the user if he wants to encrypt the file or folder (This dialog can be disabled by adding '"dontConfirmPlaintextOperation": true' in %LOCALAPPDATA%\Boxcryptor\volume.db)
When disabled, files or folders created in an unencrypted folder will also be unencrypted and files or folders created in an encrypted folder will also be encrypted.
PS: We will add a "Do not show again" checkbox to the message box in a future release.