Where to place debouncing circuit for remote mounted buttons and rotary encoders
The debouncing (and any noise filtering, ESD protection circuits) should be on the main PCB. 

The switches themselves don't need anything local to them, nor would be be optimal to have additional circuitry there. 

Edit: If the Gray code encoder is active (optical or magnetic) some remote circuitry might be useful- certainly supply bypassing, maybe some series resistors on the outputs, perhaps even a local supply regulator.