First: as the appeal opinion clearly states, there's still an open case against Ulbricht for the Force-related murder-for-hire scheme in Maryland. The charges have not been dropped.
Second, evidence of the murder-for-hire charges was presented in court. It was an element of the conspiracy charge. Not only was it presented, but it was presented in a way that Ulbricht's defense was obligated to rebut it.
Finally, the murder charges were presented again during sentencing, and proven to a "preponderance of evidence" standard during that process as well.
These details are all spelled out in the appeals decision.