This is not strictly a Direct Broadcast question. You would do better to ask such questions in the seadas or algorithm forums.
Are you referring to Level-2 products generated with SeaDAS? The missing value for nLw is 0 for both SeaWiFS and MODIS, not -32767, so perhaps I misunderstand.
There is no explicit cloud flag for SST. Again, I assume you are referring to Level-2. SST masking is controlled by the SST quality flags. For more information, see:
http://oceancolor.gsfc.nasa.gov/DOCS/modis_sst/