STAR - GOESR Vegetation Health :

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MSG/SEVIRI -- NDVI Composite with/without Cloud Mask

The figure above shows 7 days maximum NDVI composite by using CM or not.
The major difference is that if cloud mask (CM) were not used, less observations (images) will be used for NDVI composite.
If the could mask were used. for some regions frequently covered by cloud, the composite NDVI map will have holes because the CM algorithm may always identify those pixels as cloud. This often occurs over tropical forest or along Intertropical Convergence Zone (ITCZ).