It seemed as though the hash was not changing even after re-caching the skin set, so I dug into the output class and found the following:
$this->antiCacheHash = md5( IPB_VERSION . $this->settings['board_url'] . md5( $this->settings['sql_tbl_prefix'] . $this->settings['sql_pass'] ) );
Which means that its fairly pointless, as it will only realistically change when the site owner updates their board.
The hash should change whenever the skin is updated. I had a look through the core caches, and we already have a cache entry for each skin in "skinsets" under "set_updated".
I would imagine its a very simple change, that requires no extra queries, to have the timestamp of when the skin was last updated added to the hash, then whenever someone edits their skin files, changes will be reflected straight away as the hash will change.