Without the full translated transcripts and ditto police files we are shooting in the dark.
I say tomayto you say tomarto.
I doubt that anything substantial of an incriminating nature would have been left out of the prosecution case, which was reflected in the SC ruling.
If anything, the reverse might be true - i.e., the defence appears to have been little more than an assumption that the case would be thrown out due to lack of evidence. What is not clear to me is whether they had - or could have applied for - the resources at their disposal to mount an effective defence or not.
The full SC ruling is online, albeit in Portuguese. Concerning the transcripts (if you mean of the witness testimony), 45 witnesses gave testimony during the course of under three days, which allowing for lunch breaks, appears to have been quite a marathon, so I doubt that the full transcripts would have revealed much more.
The police files might have been interesting, but once the Faro boys took over from Portimão (after only 4 days), with 11 arguidos, heavy-handed interrogations for at least some of them, summary statements in reported speech - there might not be a lot that was officially recorded.
Out of curiosity, I would have been interested in the forensic lab report - but the bottom line would still have been the same.
This isn't an appropriate thread to make a list of all the things that I find jaw-dropping about what IS contained in the ruling as it is.