Even offhand, the core book Cyberdeck, as I understand it, applies to all Computers rolls, so that applies in Tharkold, PP, and CE, and sometimes the Nile. (Weird Science is the sometimes-Y of reality. You can almost always say, "And sometimes the Nile.") I figure as we get newer, even shinier Cyberdecks, their benefits will apply to a lot of lower tech networks, too. But it is true that Computer type stuff is kind of weirdly limited compared to anything else. Like, most Faith-based things might be a Contradiction in many Cosms, but it's still possible. The computer side of things (including spells like Scrambler and EMP) just doesn't apply in the realities that don't meet the axiom, and that makes it a lot harder.
What I'm really trying to say is that I, too, look forward to learning how this might be addressed, because frankly, I've got nothin'. (Except maybe the fact that All Of Computing is one skill, so you have plenty of room left to also be good at, like, Fire Combat, or even more easily, Alteration and Divination. That definitely helps keep a hacker character viable, even if the hacking itself is a sometimes thing. I mean, that's honestly true for almost all of the non combat skills, one way or another. They just don't come up every Act.)
Bringing groups with you in GodNet makes perfect sense to me, though, and honestly seems like something other systems could have done if they'd just thought of it. Though I like it even better in TORG. And despite the above, I'm really hoping there are some GodNet oriented spells and miracles. Since you can learn those as part of something bigger, it seems more OK for them to be more limited in application, and the concept is just so cool.
Honestly, the CyberPapacy is the one realm I can imagine playing a whole campaign in.