Yes that's intentional. Folders don't take up much space on their own, only a few bytes, and at most there will only ever be 4096 directories. Also those folders will get reused again as soon as visitors come to a page.
I will also mention here that if you use the Memcached driver, when you clear the cache Memcached still says it has things in the cache, so the stats on the Admin>Cache page may not be correct. (Technically Memcached doesn't actually delete items, it just marks them as expired.)