I had to write my own patch that got rid of it. Its been a while but i think that # is also used in determining the final minify name (md5 hash) which is probably not a good idea since every time it does a new minify on the same files you will get a new name which will break tihngs like cache plugins if the times arent in sync (missing files). And then there is the issue with those who crawled your page will find your minify js/css file(s) are now gone and will potentially flag the site as suspicious since these files keep disappearing every xx hours/days.
There are a few of us here who have made our own forked versions of this plugin and one day we might just merge them.
I havent worked on this plugin for several months now so i forget all the things i’ve added or patched but it works very well in every way now.