Sharing the OP’s position, and having worked in a biochemical technology development lab in grad school, I don’t think that’s quite right. Structural biology is disproportionately seductive as a data source because we are such visual creatures. You “see” it so it must be true. I’ve definitely been guilty of it while looking at protein structures, I doubt anyone in the field hasn’t. Hell there used to be 3D rigs you could buy with IR activated LED shutter glasses so you could see structures in 3D on your monitor and “better understand” the structure.

It’s easy to get misled, proteins are incredibly dynamic in solution. Binding pockets appear and disappear, change shape, add and remove water. Given a structure of an unknown enzyme, with little to no biochemical characterization, you can’t tell what the catalytic mechanism or rate is. You probably can’t tell what the crucial residues are for binding at all. You may be able to tell the binding pocket, and... generate some hypotheses!

That’s not to say protein structures aren’t helpful, they are! Especially things like co-crystals with drugs can help study that specific interaction. But I think the OP is totally right, we should back off strong conclusions on structure alone. It’s a great hypothesis generator, not a final answer in and of itself.

The awesome part of cryoem at atomic scale is that we can now get MORE hypotheses generated faster with tougher proteins than with X-ray crystallography and other methods.