Regarding the Rotary encoders Richard covered it 100%.

With shielded wires I am pretty sure you won't have any problems. Forget about R's and C's, just read two times the switch state and your are done with debounce.

As for long or short wires acting like antennas, well, the general statement "long wires act like antenna" is not quite right. It depends on the frequency we are talking about. For example, 10cm may seem very short, but this is an antenna for 750MHz and the 10m is an antenna for 7.5Mhz. So, which one may be a problem for you? It depends on what signal sources you have nearby, right?

Best way to deal with all frequencies is both cable shielding and metal case box wherever there is a possibility of interference.

But I think we are getting crazy on this...

Ioannis