Civil and criminal trials are totally different. It's common for people in civil matters to assert their 5th Amendment right to be silent when there is a criminal investigation underway. The fact that the Trump matter and Watson's issues were different highlights this point. In the Trump matter, Eric Trump "took the 5th" on questions regarding his knowledge of an attempt to subvert tax laws by calling compensation paid to the company's CFO "scholarships" for his children. That's not "paperwork" questions. Those are questions about a criminal conspiracy to avoid paying taxes. Taking the 5th during the civil depositions, to avoid exposing himself to further questions from the criminal investigators, was a smart move on E.T.'s part.
Regardless, you don't send folks to criminal trial for taking the 5th during a civil deposition because to do so would neuter the right. You do send them to a CIVIL trial to sort things out in the civil matter. Which, barring settlements, I'm sure will happen.
Only the grand jury knows why they decided to bring No Bills on each of the 9 potential criminal charges (8 of which were misdemeanors). If I were to guess, and it would only be a guess, it would be because they felt that the evidence presented did not meet the required threshold for charges to be brought. Also, during a grand jury, the defense is rarely (like never) allowed to present a case. The prosecutor alone presents his evidence and the grand jury decides if what he/she has presented is enough to bring charges. So, when you get a No Bill, the grand jury must have thought the evidence was ****.