The AFNI programs, when input-ing NIfTI files that have scale factors (NIfTI field scl_slope != 0), automatically convert the NIfTI data to floats. They do not leave the NIfTI data as shorts plus a scale factor, because AFNI internally is not set up to deal with the NIfTI scl_inter field; therefore, the scl_slope and scl_inter fields are applied immediately on input, if scl_slope != 0.
Now, you could rescale the dataset back to be stored as shorts by doing something like
3dcalc -a zork.nii -expr a -prefix bork -datum short -verb
Hope this helps.