All I know about the forensics is that this is what is in the reports.
"...why were they not indicted..."
My only guess is good lawyers. All that evidence doesn't say who killed jonbenet, only that something doesn't add up. They can't convict on that, I don't think. DNA would be key, but if one of the Ramseys did it then it may never be revealed.
Were their lawyers allowed to present alternative evidence to that of DA Hunter and the police? I don't know. If so that was fortunate for them because most often, so I hear, that isn't what happens in a GJ.