They're the 11.9V supply line and are daisy chained from the sound board to somewhere else. If you rewire as you suggest and then disconnect J2 from the sound board for test/diagnosis/repair, whatever component is daisy chained on the 11.9V supply wire will be lost. The sound board should not be wired such that disconnecting it affects functionality of other components in the game.
Highly suggest you do not separate them as it creates another point of failure. Those two wires need to be physically connected together for best connectivity.

Pins 5 and 6 are the same point. I bet if you remove the board the pins are tied together on the back side with a common solder pad. The problem with two wires on one pin is all the current is now all on that one pin. I'm sure it's fine in that the current for both wires is not exceeding the design capacity of the one pin. The schematic shows one wire from pin 5 and one from pin 6.

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The 11.9V red-green wire comes from the solenoid driver board to the sound board then daisy chained to the MPU board for the valid power detector circuit.
If the wires were separated at the sound board connector, the game will not start if you disconnect the sound board because the MPU board wouldn't be getting 11.9V supply. If one of those connections at the sound board starts becoming bad (loose crimp terminal, fractured solder on the pin header) then you have intermittent game boot issues. Also if you had to send your sound board out for repair, you wouldn't be able to start/play the game in the meantime. That would be pretty undesirable. Imagine operators with games on location in this situation that had to take their sound board back to base for repair.

What problem are you trying to fix by separating them?