So..... I couldn't take it anymore and decided to do something about it.
In another thread I was directed to this: http://forums.sinsofasolarempire.com/406614/
IskatuMesk has already gone through and remastered several sounds and offers them up for all to use pending credit is referred back to him.
I started to try and create an audio MOD but my meager attempts merely served to crash the game, so I just made a backup copy of the original sound folder and the replaced some sound files one by one. I mostly focused on the gun fire from the capital ships as that is most noticeably lacking.
It still took longer than I thought it would to do just that, so I couldn't imagine having to start from scratch with no sounds.
I can upload to some web space if anyone is interested. It's my first stab at it, but I'm fairly happy with the results so far - that and coupled with hardware audio acceleration and this game is finally starting to sound good.