Can you differentiate calcium deficiencies in skeletons from malnutrition vs the effluxion of calcium in bones due to inappropriate pth release?

That's why I mentioned it would be hard to solely diagnose childhood malnutrition on xrays.

Only in severe cases where you develop rickets, and even then it might only show possible evidence. At that point you MAY see see early signs of arthritis and suffer from symptoms similar to arthritis and be more prone to fractures. Unfortunately there are many causes of this including but not limited to autoimmune conditions, thyroid/parathyroid conditions and bone cancer, so it is hard to go straight to malnutrition being the cause.

You could also be found to have reduced growth compared to your expected, eg height, weight. But there's also so many other factors dictating growth.

Malnutrition in childhood has been found to have higher rates of widespread conditions in adulthood including diabetes, heart disease and arthritis. Doesn't mean you will develop them but you would be at higher risk of it. And again the issue is that there's many factors causing those conditions as well.