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What are the differences in cloud screening between the Dark Target and Deep Blue algorithms and why is the screening different?

The cloud screening procedures for the two products use similar principles but different tests due in part to different bands used in the retrieval algorithms and different pixel resolutions used in algorithms. Really 'cloud mask' is not 100% correct as a term, they are more like a 'suitable pixel mask', and both algorithms have different requirements for pixel type (e.g. Dark Target has  a surface brightness criterion).

How do you screen for clouds?

The cloud screening in the MODIS dark target aerosol algorithm is a series of internal and external tests, and is different over land and ocean. The details of the cloud masking scheme is described in section A2.2 of the ATBD. The Collection 6 aerosol products contain a new SDS called “Aerosol_Cldmask_Land_Ocean” which characterizes each 500 m input pixels as “clear” or “cloudy”