Yes, with a powerful enough source you can resolve protons, that's true. They didn't make such a claim - they listed a run-of-the-mill instrument in their methods section that would not have been capable of this.

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.

Raleigh's criterion says hydrogens should be just on the cusp, at least with home source xrays. Not sure about synchotron.

I mean, I know this is possible- I've definitely seen maps from very high quality (<.8A) crystals that clearly had defined bumps on the heavy atoms that were where you'd expect the hydrogens to be, and later on, neutron scattering confirmed it. But the only times I've seen this it was world-class competitive groups trying to elucidate the specific enzymatic pathway for a protein of industrial interest.