The largest technological question we raised in our appeal (which the courts refused to consider) was what constitutes a "search", i.e., whether law enforcement can demand the encryption keys of a business and use those keys to inspect the private communications of every customer, even when the court has only authorized them to access information belonging to specific targets.
The problem here is technological: until any communication has been decrypted and the contents parsed, it is currently impossible for a surveillance device to determine which network connections belong to any given suspect. The government argued that, since the "inspection" of the data was to be carried out by a machine, they were exempt from the normal search-and-seizure protections of the Fourth Amendment.
More importantly for my case, the prosecution also argued that my users had no expectation of privacy, even though the service I provided – encryption – is designed for users' privacy.
If my experience serves any purpose, it is to illustrate what most already know: courts must not be allowed to consider matters of great importance under the shroud of secrecy, lest we find ourselves summarily deprived of meaningful due process. If we allow our government to continue operating in secret, it is only a matter of time before you or a loved one find yourself in a position like I did – standing in a secret courtroom, alone, and without any of the meaningful protections that were always supposed to be the people's defense against an abuse of the state's power.