A cap is not useless at all. In the long run it will help to save your electrical system(trust me there are thousands of “caps” all over today’s cars and for the short term it will keep you battery from robbing power from other devices in the car when your amp needs an inrush of current.
IE, I’m sure everyone at some time has turned on their lights and hit a note that dimmed them. With the right wiring and a cap this issue can be resolved (for the short term).
Also, I would 100% have to see you increase the output of an amp by taking a cap out. There had to be something wrong with your wiring, cap or usage to have this happen.