Mumetal is for shielding devices from constant magnetic fields. It won't help protect against EMI any better than a metal box will, unless the EMI takes the form of low frequency magnetic fields.
To protect against intense EMI, you need to enclose the circuit in a metal box - typically with a conductive gasket between the two halves - and also prevent EMI entering via the inputs and outputs. This is done by a combination of designing the input and output wiring so as to minimize EMI pickup, any by using RC or LC networks in the input and output circuits.
If you use a crystal, you should connect the metal case to ground if you expect EMI to be a problem.