The best solution for this is to not include the hash in your filename (I assume you are rendering to filename_#.ext). You'd just need to remove the '#' from your rendered filename, then SquishIt will use querystring invalidation by default. This will only keep a single copy of each bundled file on disk. If querystring invalidation won't work for you there is also a relatively new option that allows you to place the hash into the path as a directory, then scrub it out with an IIS rewrite rule.
For more on SquishIt's support for different cache invalidation strategies read this