Measure EMI Pre-Production

EMI is very difficult to predict, but there are many things you can do in design to minimize effects and predict where problems will be. Clocks, CPUs, comm ports, and other components have known, regular oscillations. Those frequencies are often the ones that end up being 'transmitted', so that is a good place to start looking for problems. In addition to the mitigations listed in that article, like good grounding practices, you can also put local shielding around components that you know will be noisy. Housing design is also critical. If you are worried about emissions, go ahead and build an EMI tight box. This takes more thought than just throwing a product in a housing, so cost will go up. Using shielded wires internally can make a big difference. I've also seen boards with multiple ground planes embedded as layers near the top and near the bottom, with all the noisy traces running on layers between the planes. Methods like that can greatly complicate boards and run up cost.