Did you miss all of the explanations laid out? There was intervention Diane Carey mentions this in one of her novels, and the young Vulcan bully mentions a clinic.
Then one has to consider the Preservers and what they may have done in seeding the galaxy, and please remember that Star Trek has no problems bending science to tell the story. You want to really get screwed up look at the impossibility of mapping all the moving subatomic particles in a mass, then converting that mass to energy and reassembling that energy as matter it the end point. It simply cannot be done. And you can't stop that motion. And even if you could map the matter and convert it to energy, you would likely stop all the electrical activity in the body. Successfully killing the person.
Star Trek isn't the only place where gadgets and devices cannot function. Lightsabers can't function either. Photonic energy cannot be rendered coherent, so lightsabers would simply pass through one another. If you want hard science in your science fiction. Stick with Arthur C. Clarke, and Isaac Asimov.