Well Bongiorno appears to have said that judges involved in previous trials will be investigated. That's ambiguous. Firstly, "investigation" could just as easily mean investigation by professional bodies, as opposed to a criminal police investigation. And secondly, does her definition of "judges" extend to figures such as Mignini and Comodi, who technically are members of the judiciary?
I think that there should be investigation of the conduct of the courts in this case, particularly the Massei and Nencini courts. I think there's a strong case to answer that these courts unlawfully disallowed certain evidence, unlawfully failed to mandate proper disclosure to the defence, and made unlawful rulings on certain key items of evidence and testimony. I think they should be held accountable on these issues, and if they are found to have been in error, then the professional judges involved should be severely professionally sanctioned as a result.
But, as you say, there is potential for criminal investigation as well, though not of any of the judges. I think not-a-real-doctor Stefanoni may well have a case to answer over her court testimony (possibility of perjury and obstruction of justice?), and that maybe even Mignini and Comodi have criminal cases to answer as well.