In looking at the chlorophyll data at the NOAA Viz Lab website:  https://www.nnvl.noaa.gov/view/globaldata.html#ALGE,  the gray speckled areas are most likely clouds as you suggested.  The NNVL site is providing weekly/monthly/yearly composites of daily data.  Missing 'blocks' are most likely due to the mapping service failing to render a tile for your web browser.

With daily chlorophyll-a data overlaid on true color,  you can see several areas of missing data primarily due to clouds/aerosols, sun glint, and quality filters:

By compositing daily optical products into weekly and monthly merges, areas of 'no data' are reduced and present a more complete snapshot of our oceans.  The satellite's orbit procession will provide next day coverage over the swath overlap and sun glint areas reducing the 'no data' areas in multi-day composites due to persistent clouds at the time of observation.

The oceanographic products come in two quality states:  near real-time and science quality.  To my knowledge,  the quality of data transmission from the orbiter to the downlink station is not quantified [or a significant issue] in these products.  More information on NOAA Ocean Color VIIRS satellite products is at https://coastwatch.noaa.gov/cw/satellite-data-products/ocean-color/near-real-time/viirs-single-sensor.html