It is still a VS2 regardless of the inclusion type, so I don''t think the value is affected. An indented natural is just a place where the orignal "skin" of the rough wasn''t quite cut/polished out in order to maintain the size/shape and is slighly below the surrounding surface level. At VS2 clarity, it means that this spot was slightly difficult to find under 10x magnification, so no worries about seeing it with the naked eye.
Usually a natural is near the girdle, so if this is a diamond you are interested in purchasing, check to make sure the girdle is not too thin at that point. Naturals can often be covered by a prong, as well.
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