Could you provide more information on how the module was slowing down your site and more about "I disabled it but found out the css add-on was still effective".
The latter sounds like there might be a caching plugin active on your site that didn't refresh when disabling the module? Once it is disabled, the code that has the Custom CSS tools (and functions to display it) aren't called in at all.
To more directly answer the question, the custom CSS is stored as a custom post type within WP and the revisions are like any other post. Having them in the database doesn't impact performance any more than revisions on posts in general.