While I realise this hasn't been posted in for a long time, it's one of the first results on google when trying to find out how to beat superfortresses, so seems like a reasonable place to put this information. A good way I've discovered, which I haven't seen documented anywhere, is to use the Spire rams. Two mark 2 ones appear to destroy all the fortress's hit points. Of course, you need an appropriate asteroid first, and then can't use it for anything else, but if you accept that then it's a lot easier than nibbling away at it with bombers.