Dear Petr,
you can find the current versions of the CM SAF documents (including the Product User Manuals / Validation Reports (2010 being the latest available report at the moment) / Service Specifications (SeSp)) at the CM SAF homepage (www.cmsaf.eu -> Publication and Documentation -> CM-SAF Documentation).
Yes, the value of 255 in the netcdf CFC file is the missing data value. This means that, for some reason (e.g., to few observations to calculate the average), no data is available and this pixel must not be considered for further analysis.
The information that 255 corresponds to missing data is included in the netcdf-file as the '_FillValue'-attribute of the corresponding variable. This standard (defined in the CF Convention) allows software that reads netcdf-data (e.g., panoply) to automatically account for the missing data.
Unfortunately the ncdf-package of R does not consider this attribute, however, the provided scripts should analyse the '_FillValue'-attribute and set the corresponding pixels to NA.
Hope this helps, kind regards,
Jörg