Because the murder charge is factually complicated, the Silk Road charges are simpler, Ulbricht will serve a long prison sentence if convicted of either set of charges, and introducing the trickier murder charge risks the credibility of the rest of the charges with the jury?

That doesn't sound plausible - US prosecutors are notorious for piling up charges (even when there is little chance they will hold in court), to increase the maximum possible sentence the defendant could server, to make him/her plead guily and settle (e.g. the story of Aaron Swartz).

This is similar to the logic people applied to the Reiser case and their failure to charge the "serial killer" who "confessed" to Nina Reiser's murder.

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.

Furthermore, if the prosecutor wished it, the grand jury would indict a ham sandwich.

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.

It is also possible that the evidence was collected illegally.

Also true!