My deprecated dcm2nii software does convert the DICOM time stamp to the number of seconds since midnight in the header's description field, whereas my modern dcm2niix copies the text verbatim from the DICOM header, so follows the DICOM header. Consider a DICOM image where the AcquisitionTime element (0008,0032) is "134808.242500". If you use fslhd to examine the header generated by my old dcm2nii you will see
  descrip TE=2.7;sec=49688.2425;phaseDir=+
reflecting that 1:48pm is 49680 seconds after midnight. 

On the other hand, dcm2niix reports
  descrip TE=2.7;Time=134808.242;phase=1
and it will generate a BIDS JSON that reports
  "AcquisitionDateTime": "2008-06-17T13:48:8.250000",