I run a large WordPress installation (~17 million pageviews/month) and WP Super Cache does an amazing job with it!
I use preload and set our supercached files to not expire which results in having 10,000+ files supercached at any given time. This reduces load on the site greatly since many of the older posts do not get updated frequently.
Where we see issue, however, is when we need to clear the cache for some reason (template changes, etc). The large number of files and folders in combination to the heavy load of the site often times out the administration page when trying to delete cache.
What we have begun doing is simply renaming the cache folder and allowing a new folder to be created in its place. This result is immediate. We then delete the old cache folder during off-peak time for our site.
Wondering if it makes sense to do this by default with WP Supercache?
When the "Delete Cache" folder is pushed it renames the cache directory and a new one is created automatically and the old directory is queued for deletion over time (perhaps making use of the preload cron?).