Removing old post revisions still works fine, but WP-Optimize now always indicates that database tables need to be optimized. If you select "Optimize database tables" and click "Process", it will appear to have worked, as the status then changes to "optimized" for all tables. However, on your next visit, the red "Need to optimize" warnings come back.
To be honest, I'm not positive that this started at 3.0.1 - it might have been at a lower WP revision, but escaped my attention. I get the same thing with 3.01 and 3.03.