I've had my stereo in my car for 2 years now. (Rockford T1500.1bd wired to 1 ohm which is about 1500-1800rms depending on the song) I never run a cap and never will and my alternator is just fine and i drive with my lights on during the day sometimes (mostly when cloudy should be a law in every state especially when raining). My alternator is constantly running and it has never failed. Hell the Alt in my truck lasted damn near 20 years before it finally gave way last year and it had pretty good sized stereo in it and multiple battery draining instances.
If anything Caps are worse for your alternator than adding another battery. Constantly charging and discharging is not good for your alternator at all. Plus a battery is cheaper than a cap and can have more reserve.