The reasons vary. Sometimes the speaker harnesses/plugs get lost or become too short to use and are soldered to the board because replacements are kinda hard to find or are too expensive. In more than a few instances, the factory speaker wire is considered to small and a thicker gauge is substituted, especially where high current or low resistance loads are being used.
One tip: most (not all) of the old factory plugs can be popped open to replace the wires. Don't try to use too thick wire though or they will never snap back together.
As far as I can tell, the wiring harness is the only weak point on the old PPI M/AM or Pro Mos amps.