A cap on a GPIO pin will cause a rising/falling edge curve instead of a sharp change. It just means it’ll register the button press, or encoder wheel rotation, 2PiRC seconds later. 2Pi * 20k * 1000pF is a ~125uS delay in the register of the edge, which is only relevant to signals oscillating in the kHz range. You are unlikely to be turning the encoder wheel, or cycling buttons, that quickly, or even within a couple orders of magnitude of that rate.?

-Mark