It all depends on the forcefield you are using. United-atom forcefields like GROMOS will only need polar hydrogens since all others are considered in the parameters for the heavy atoms they are attached to. Others, like AMBER or CHARMM, are usually all-atom and will add all. I never used SPDBViewer/DeepView, and I'm usually against using molecular visualization tools like SwissPDBViewer and PyMOL for purposes other than visualization. My suggestion is to try and use GROMACS, which is free, fairly simple to install/compile and use, and is suited exactly for this kind of analysis.
Edit: noticed after writing the answer that this was an 'updated' question by the Biostar Community user... anyway, the answer stands. Someone might find it useful.