It sounds like there's an audio amp in there somewhere (if the system were a typical unamplified speaker setup, then you should get NO sound without something hooked up to JAMMA as the speaker is physically disconnected). The input of the amp will pick up all sorts of stuff if nothing's hooked up. Best option would be to unhook the power from this amp if you're not going to use it.
Plenty of candy cabinets have been MAME'd or otherwise altered, but each candy is different inside, especially those from different manufacturers. Your wiring and power supplies look absolutely nothing like that found in my SNK Neo 29s, for example.