I'm sure that proprietary software has come up in lawsuits before and the prosecution/defense teams were allowed an audit and inspection during discovery. After any findings are presented in court, I'm sure there is a legal means to either restrict the filings/documentation submitted in court or whatever.

There is no way this is the first time a private entities code has come under scrutiny in a courtroom, so there should be plenty of legal guidelines/precedent to follow on how to handle this.