Yes. It is not necessary to keep the spam messages in your e-mail program’s spam folder because SpamSieve stores the information that it has extracted from the messages elsewhere.
Before you delete any messages, make sure that you have corrected all the mistakes. To make it easier to find any good messages that are accidentally in the Junk mailbox, you may find it helpful to sort by subject or to separate the spam messages by color.
To manually delete old spam messages, you can simply select them in your mail program (using Edit ‣ Select All may help) and press the Delete key. In Apple Mail, you can hold down the Option key when pressing Delete if you want to delete the messages immediately rather than moving them to the trash.
To automatically delete old spam messages, please see the Automatically Deleting Old Spam Messages page.