We have prepared an obfuscated second tier communication array conforming to all the requirements of plausible deniability which can be installed on your vessel. Let me start from pointing out obviousness. You cannot simply install a sophisticated communication and sensor array on a transport vessel. It is like shouting "I have something to hide!" during an inspection. Even the most basic scan performed by a drunken LPI will detect it.
What you need is, instead of one sophisticated high-technology module, a set of remotely connected ordinary functional modules that during scan will look like nothing unusual. For instance a life support control module with extended memory drive and stronger central processing unit, fuel consumption control module with custom extensions and power capacitors, starboard engines control unit with supposedly redundant network interface... All these modules upon inspection will look perfectly normal like any broken module repaired with random salvaged parts. What an inspection will not be able to detect is that all these remote nodes when being connected to the ship internal network and controlled by a managing program ran from main system console will act like a military-grade communication and cryptographic array.
You might be worried that during a prolonged inspection your investigators will find our software on your ship and thus learn about the obfuscated array. I wish to assure you that there is little chance for that. Our software will be stored in sectors of your memory drives that are tagged as empty space. Using high entropy algorithms we will fill it with random data so it looks like remnants of deleted files. However, upon activation after specifying leading sector and correct decryption password a virtual drive using these sectors and containing our software will be mounted in your system and allow you to run our software securely and safely.
Once we detect you using Liberty or Independent Worlds trade lanes you will be approached by our vessel and necessary alterations will be made in space.