What matters with speaker cables is resistance. You want to minimize this. As long as you are using the correct awg of wire and staying with the recommended length of that awg, then its safe to say there will be no difference.
For example if you run 50 feet length of 18 awg wire to your surround speakers then you are running the risk of the resistance getting to high. This could cause output problems as well as changes in the frequency response.
In the case of the internal wiring in the subwoofer, it is going to be a very short length. The supplied 16 or 18awg (whatever they use) will be sufficient.
