The Cyberware skill already reduces trauma, regardless of how bad the operation is. The hardware diagnostic present in the game simply increases the cyberware skill, resulting in less trauma; it sounds like the same effect could be rendered simply by hiding the game mechanic involved and leaving it to the player's imagination.
That said, I like the idea of a software diagnostic; cyberware probably already gives feedback in some form, and a software interpreter could probably pull off the same effect as an external diagnostic system. Maybe there ought to simply be, as you say, a bio-comp or On Body Computer (to use Palladium references) and varyingly expensive cyberdoc utilities.
Norton Spineware - A high-end debugging software which diagnoses all common hardware problems, performs standardized tests according to schedule, and auto-updates at all hospitals.
Regex Utilities - A deluxe suite of tests, drivers, software fixes and convenient programs for the serious cyberware user. While expensive, it is within reach of most consumers. Replaces the original operating system of all cyberware on the body. Now with fewer conflicts. Includes Regex Command, Regex Cybersys, and Regex Planner Deluxe.
Regex Cybersys - Sold separately from the deluxe suite, the Regex Cybersys cyberdiagnostic program is a competitor and a crowd favorite. Nearly as good as Spineware and far less expensive. Does not include Planner Deluxe.
Silvertech Plus - A suite for the prevailing operating system which nearly all cyberware uses. Includes an installation disc of Silvertech Official Release 6.5, the operating system cyberdocs trust! Patches Regex Cybersys and Regex Planner Deluxe to operate within a Silvertech environment.
Jolly Roger Imperial - The open source operating system of choice; runs pirated versions of all other cybernetics software. Very high security, free for download. Copyright lawsuits are pending against Jolly Roger Software; purchase of this OS is prohibited by law.