Which tool are you referring to ? For the sbsrender, this is normal because the *.sbsar files are tied to the bit depth. Although newer versions have option --output-bit-depth wich allows you to change the bit-depth of the result (not the bit-depth used to compute the render).
For sbsbaker, I've re-installed a 5.6 version of the batchtools and I cannot see any option related to the bit depth with for sbsbaker - the bakers compute in 32-bits float and the result is cast to highest information bitrate the storing format supports. So, if you're saving to PNG, you should have 16-bits/channel images. I have that behaviour with either the tools from substance designer 5.6 or the tools from substance automation toolkit 2017.2.1.