Most of the time hydrogens are placed in calculated positions because you know where they are and it also reduces the number of parameters needing refinement. I

Most of the time hydrogens are placed in calculated positions because you know where they are and it also reduces the number of parameters needing refinement. In good datasets hydrogens will show up in the density map (aren't all datasets good now in the age of area detectors), and you can refine (possibly with restraints) those hydrogens that you are uncertain about.