Does voltage rating increase on ceramic capacitors have any effect on the performance of the capacitor?
With high value ceramics like that, a higher specified voltage will mean a higher capacitance at your operating voltage. That is, the capacitor won't lose as much of its zero volts rated capacitance to voltage coefficient.

In decoupling applications, a little extra capacitance is a good thing. Given the tolerance of these capacitors, it's unlikely the circuit has been designed to rely on a particular reduced value.