Aerospace software (which would include anything that runs on a ship's computer) is very expensive to build because it requires very heavyweight quality control processes - and flight testing to ensure that it works and everything integrates correctly together. It's not like pirating a game.
In practice, avionics, fire control and other similar systems are more like embedded systems than a PC or server. While there is (theoretically) a general purpose computer (or many) built into the system the software is going to be relatively static and not shipped as an end-user installer. In practice, doing these updates might require a specially equipped computer and an image downloading/diagnostic tool from the system's vendor.
I would imagine aviation certification authorities would be quite horrified by the notion of end-users installing random software onto the flight control computers of an aircraft (or spacecraft, for that matter).
Any software application for such a platform (fire control, navigation, jump control etc.) will require extensive system, integration and flight testing before it can get certified (or even trusted not to screw up catastrophically). It is also likely to require significant customisation work in order to convert it to run on any new ship or configuration, which would require access to the source code.
Generally, we can assume that installing new software into an avionics system would require skilled technicians, and actually developing the software or porting it to a new configuration would require significant testing work including flight tests. Note that traveller doesn't really specify this kind of canned configuration, but it's pretty much how it works in reality. The hardware is largely shipped as a black box, with software updates being released occasionally by the vendor, and typically only in response to serious bugs or major feature releases of the system.
The exception to this would be modules that are available as optional extras for a given avionics package. In this case, the software might be possible to pirate, or even just unlock with the right activation code. However, you would have to find someone that had a firmware image in the right configuration. There might well be a grey market for such things.
