Every time a user/bot sends a comment in a specific post or page Spam Protection checks if that specific user/bot has visited for at least X seconds ( this value is customizable through the Options menu ) that specific post or page.
If that user/bot has not visited that post for at least X seconds the user/bot receives a custom message. ( ex: “You are posting the comment too quickly. Slow down.” )
You can also set a maximum time limit, each user/bot has a maximum time limit within which he has to post a comment.
You can browse all the blocked comments under the Spam Protection menu voice, so that you can actually check how many comments this plugin has blocked.
And you are right, its a cookie based plugin.