I don't think the words "trade secret" fit - the correct term is "Intellectual Property" (IP).
Anyone outside of the parent organization that gets access to Airbus or Boeing IP will almost certainly have to sign a non-disclosure agreement (NDA) that will prohibit release of that information (or suffer the legal consequences - which are punitive in the extreme). I'm sure the same is true of employees of those same corporations, probably part of their employment contract.
IP would cover any aspect of the aircraft design, not just the FBW part. Obviously you can infer certain behaviors from what is visible externally, or published within the public domain (training information on systems for example). The core algorithms and code though are sure to be closely guarded.
- GY