Replace a 500Kohm potentiometer with a digital one
The circuit in the Commodore Paddle is connected as an R/C (resistor-capacitor) circuit. It uses the combination of P1 and C1 to form an "RC time-constant" where the computer discharges the capacitor, and it times how long it takes for R1 to charge-up the capacitor. The lower the resistance of P1, the shorter time it takes to charge C1.

And the other section P2 and C2 work exactly the same way.  Alas, the variable resistor is NOT used as a true potentiometer. If it were, then you could substitute a 100K digital pot without any problem.

If you want to substitute a resistance of 100K instead of the original 500K, then you would need a corresponding capacitor that was 5x as big to maintain an equivalent RC time-constant, at least in theory. 

It seems like a rather awkward way of controlling the paddle inputs.  You didn't mention what is controlling your digital pot(s). It may be more expedient to replace the pot with a field-effect transistor (FET).  Or simply monitor WHEN the Commodore discharges the capacitor and then wait an appropriate length of time (proportional to the "position" to apply a voltage to SIMULATE the RC time constant charging.