It's onyx, it's a natural stone, what you are seeing are minute inclusions in the stone. The highly polished surface just allows them to be more visible. I wouldn't exactly call it a defect in the dial. If the only way you can see them is through a loupe at a particular angle, and if you haven't noticed them up to now, I wouldn't be too concerned about it. It's all natural and common in any kind of decorative mineral. Just look at diamonds, there are minute inclusions in almost every diamond under magnification, the fewer there are the higher the cost.
Beautiful watch by the way.
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