As such there is no limit on the number of photos that you can work with Flickr batch organize. However, your internet connection may impose some limits depending on your connection speed. The Flickr batch organize can handle batches of 150 - 200 photo or more. Flickr has clearly stated that even if you have a broadband connection, you can witness occasional slow uploads. This delay is because of the communication between the computer and Flickr server.
To see what number of photos works best for you, you may need to experiment with different amounts of pictures.