structural design for buildings. Almost no buildings are capable of surviving a direct hit from a tornado. It's possible to calculate the forces that a tornado applies, and build a structure that can withstand them, but virtually no one does it, and building codes don't require it. The likelihood of a direct tornado hit is so low that protection of property and life you'd get from bomb-shelter-like buildings are outweighed by the additional cost and inconvenience caused that building every structure that way.
The odds of a mass shooting like this in any individual school are infinitesimally small. You say nothing like that will happen in 99% of schools, but really it's more like 99.999%.