I believe this question has been answered more than once, and perhaps I should try to put in the FAQ.
1. Older versions of SSU create more cache files, try to upgrade to the latest one.
2. SSU caches files based on url, not product or category, so you will always have more cache files than number of products and categories.
3. No, urls will not end up corrupted. If cache files are deleted, SSU will just regenerate them
4. New versions of SSU always come with a cron folder which contain a cache cleaning file. You can set up a cronjob to have this file run once per month.