Is shielding the entire circuit with a faraday cage a good idea?
The MCU is not sensitive to "noise" as long as you don't have any analog circuit (e.g. ADC, analog comparator) and as long as the noise is not extreme (e.g. next to very strong and fast changing E/M fields). 
So you problably don't need to shied it from your small DC/DC converter.
You just need to take care that the power supply is clean from spikes (some ripple doesn't matter), but that's not accomplished by shielding.

If you want to protect the outside wold from your circuit shielding may make sense.