I'm playing Scion with my group and we are quite dissatisfied with the combat system (esp. melee vs. gunfighting and rolling damage) and its interaction with specific powers and mechanics (hardness, untouchable opponent and much more). We already have some house rules, but now they are up for tweaking and I would like to simulate some battles with specific parameters and opponents to gather some hard data (combat length, damage and death percentage) on the effects of rule changes. Is there software that would support me in this task or do I have to write it from scratch?
Considering that your goal here is to simulate the effects of rules changes, it is very unlikely that there is software general enough to do that which doesn't simply amount to a programming language itself.
If you would like to look at changes at a somewhat more atomic level, AnyDice is a fantastic tool for simulating just raw dice probabilities. In many cases, when simulating a battle, you can get pretty far by working up a calculation of the expected drain on resources (health, energy, etc) and carrying that along until it is exhausted.
Unless you are very lucky with Scion, then this will have to be written from scratch. I would have to question whether that was worth it. This is something to embark on in my opinion only if you would enjoy the coding challenge, and unless you have a lot of spare time before you need decisions on those house rules, you may not hit a deadline.
Most pen and paper RPG systems are designed with some basic maths (or by feel) then play-tested with humans, I've not heard of one that is software tested.
Player-written testing or simulation tools are ad-hoc and normally only look at some small part of the system. I expect there are many hundreds of Damage per Round spreadsheets for analysing games where that is important, and very many probability analysis or dice-rolling utilities. But very few working combat sims. Although here is one for The One Ring, they do exist!
For many game systems, publishing a fully-working combat sim is likely to get the software writer into some trouble with the holder of the game rights. That is because as well as the rules coding (which is arguably not copyrighted), the developer would need to code in much data from the game source books - names and effects of character abilities - that is under copyright. RPG companies can make profits from spin-off computer games and often license their content in order to do so. White Wolf have done so, so I would expect them to protect their intellectual property. Therefore, even if someone else has written an engine that expresses a large part of Scion, they most likely would be keeping their work unpublished.