But you can also pre-empt a lot of problems by designing the system around physical limitations. Many games have done that for a long time. E.g. I believe Terminus included things like mass for components, so adding all kinds of extras had a cost in fuel usage and maneuverability. So if you did build a ship loaded with the most powerful weapons, you could, but it'd also be a slow, hard to control, big target.
Mass, volume, energy expenditure, waste heat - there are lots of factors you can add to make it hard to exploit. Of course, you need to tune those factors, but it makes it less likely for really extreme effects.
I also think you should rely on player feedback and community to spot this kind of things, but that could become time consuming if you're a lone developer.
[0] http://lbrandy.com/blog/2010/11/using-genetic-algorithms-to-...