dcm2niix only reads the DICOM images, it does not modify them in any way. It does have the option to rename DICOM images with the "-r y" argument. For example
 dcm2niix -r y -f %t/%s_%p/%4r_%o.dcm /path/to/dicoms
will make copies of your DICOMs where the file names willl reflect study time, series number, series name, instance number and media instance UID. Even in this case, the data in the DICOM file is not changed.

There are other tools (including gdcm and dcmtk) that modify DICOM files: anonymizing and changing transfer syntaxes. THis is beyond the scope of dcm2niix. It only does one thing: convert DICOMs to NIfTI.