There doesn't seem to be a definitive book answer for this one. I'm actually inclined to think that this is on purpose, and there's no such skill - all such rolls should be made on
Tech-use or an appropriate trade skill.
I don't think you should add
Trade (Programmer) or
Trade (Software Engineer), because I don't believe those professions actually exist in 40k.
This is to do with universe feel. 40k Imperial and Chaos tech is mystical and badly understood; while there must obviously be software and programs, they don't see much abstract computing. 40k doesn't seem to have any common equivalent to the general-purpose computing device; almost all software is embedded control software, tied to a specific machine. I can't think of any reference in the source material to a programmer who isn't also an engineer.
Indeed, given the focus of the 40k tech-base on reproducing standard pattern devices and then jury-rigging modifications, there may actually not be such a thing as a general-purpose high-level programming language in most of 40k space - that requires a degree of technical understanding that probably only the Tau and Eldar have. Quite possibly each category of devices just has its own embedded programming language, and learning to code in it goes with learning to build and maintain the device.
So I'm inclined to think that rolls to handle programming should be on the appropriate skill for whatever device the PC is trying to modify or reprogram.