An ellipsometry system detects and/or identifies significant corrosion on glass, such as on soda-lime-silica based float glass. In certain example embodiments, there is provided a method and/or system using ellipsometry to detect and/or identify significant corrosion on soda-lime-silica based glass, so that such significantly corroded glass can be identified and not coated with a low-E coating and/or not used in applications where optical appearance is important. The ellipsometry system may be part of, or used in connection with, a sputtering apparatus/system for sputter-depositing low-E coatings on glass, so that whether to pass a piece of glass to the sputtering apparatus/system is based on whether significant corrosion is detected on the glass.