Mail Extension
When using the Mail extension, the Mark it as read setting tells SpamSieve to mark new messages as read if SpamSieve thinks they’re spam, e.g. so that you aren’t distracted by the unread count in Mail’s sidebar. When all the messages in a mailbox are marked as read, Apple Mail will stop showing a number next to the mailbox.
Mail Plug-In
When using the Mail plug-in, you can customize the actions of the SpamSieve rule in Mail’s settings. For example, to mark the spam messages as read, click the + button at the bottom of the rule sheet and choose Mark as Read from the pop-up menu.
Do not add an action that changes the color of the message, as it will not do what you expect.
Server Junk Filters
The Mark it as read feature only applies to messages filtered by SpamSieve. If a server junk filter moves a spam message to the Junk mailbox before it gets to your Mac, SpamSieve normally would not see the message, so it would not mark it as read. If you want SpamSieve to refilter message that were already caught by a server junk filter, please see the Rescuing Good Messages Caught By a Server Filter section of the manual.