As I said, this is a matter of debate. I have carefully chosen my words, and am not advocating adding hydrogen atoms regardless. And while, indeed, in some cases we really can't be certain that the hydrogen atoms are located where we put them, we can certain that a water molecule without hydrogen atoms is wrong. Unless it isn't a water molecule, but an OH- or an O2-, of course, but then this should be known from other analytical techniques and the crystallisation conditions.
From the chemist's point of view, I'd rather have all hydrogen atoms present in a chemically plausible position and end up with a structure that resembles chemical reality, even if the actual position of the hydrogen atoms could not be determined by the x-ray diffraction experiment.