In a standard setup, EGT is usually measured on only one cylinder. A probe is placed in the exhaust tube on that cylinder only - The other cylinders are not monitored.
When you do mag checks, If the cylinder with the probe is the one with the bad plug or magneto and therefore not firing, then indicated EGT drops to near zero even though the other cylinders may be firing perfectly.
If you have a multi channel engine monitor/analyser then it is easy to see which cylinder is misfiring as it will be the cold cylinder!