DO leave adequate space on your PCB for EMI suppression devices. With good EMI design practices, your circuit board may be very quiet. But to be on the safe side, leave extra space on the board for the addition of filters and chokes. It is also a good idea to add extra pads to the board in case a shunt capacitor is needed here or there.
DO NOT assume that "second sourced" parts will have the same spectral characteristics as the original. This is especially important for active components such as DC-DC converters. The fit, form, and function may be the same, but the EMI noise could be significant. Before investing in a large stock of these extra parts, plug one into your design and take it for a test drive.