I am not sure what you mean by "IDL is taking into account zero values that are used to define NaN pixels". Are the '0's' set to NaN? 0 is a valid value so in order to ignore pixels in ENVI_STATS_DOIT, you need to use a Mask (m_fid, m_pos) or set the 0's to NaN. Then those pixels will be ignored in your statistics calculation. I would use a mask since NaN pixels can cause issues in other processes.