Morning Pedro;
CPU usage of Autoptimize depends on whether or not the optimized CSS and JS can be served from cache. If not, it has to re-minimize, which indeed takes (CPU-)time. If cache can or cannot be used, depends on your site and specifically if there is CSS or JS that is unique to each page. If so, excluding that unique CSS/JS from optimization can help you bring down the amount of files that have to be re-minified. There is info in this blogpost on how to identify which JS/CSS to exclude.
Hope this helps,
frank