The reality is: charges are applied strategically in most federal cases, and, for that matter, witness lists are regularly withheld until trial. The reason this is generating outrage now is because people on HN have a rooting interest in Ross Ulbricht, just like they did in the Reiser case.
The fact that he was not indicted shows that the prosecutor did not desire for him to be indicted. Given the aforementioned notoriety for throwing everything at the wall to see what sticks, the most likely explanations for a no-bill are (1) the charge can't actually be proven with admissible evidence or (2) the suspect is a cop or (3) the prosecution of the charge would embarrass or otherwise damage the state.
We can probably rule out #2. And by the ham sandwich rule, #1 is only rarely an impediment to indictment. So that leaves #3. The state probably fears what would go public in the discovery phase if they pressed the murder-for-hire charge, and that might affect its position for the other charge.
That should make all of us curious.