I think hacking just has a problem of what people "think" it should look like, versus what people have a good idea about how it is, versus people that actually know how to hack think it should look, versus the end all be all in a video game - fun. In a game like this, I personally dont think anyone in that year is going to be hacking anything by themselves. I would imagine it would be more along the lines of AI using super computers and unlimited bandwidth to probe and investigate the systems in place at the mission area. With layers upon layers of virtual private networks disguising the origin of the inquiries.
So if anything, you would receive a mission - go to your bunker to start the AI's investigation routine on the mission area. With almost instant response, the AI tells you that its such and such manufacturer and gives you a list of opportunities to take advantage of. For example, a security system by Votec Industries has a tier 1 backdoor that allows you to take control of Turrets as soon as you are able to put the routine into a break point. A security system by Intel causes the area to overheat. etc. etc. The break point for these systems being an on site delivery method that is directed by the AI in a "witcher sense" kind of display.
As you go through the game, you get different pieces of tech from different corporations and take them back to the AI to be researched. This allows you to climb a tech tree up until master utilization. Then your list of available options for what you can do on the call back response from the AI in the mission area is expanded. So from the example, Votec Industries, you can now control the specific targets, the doors, the cameras etc. This works for Cybernetics as well, as long as you have some wireless capability built into your own cybernetics.
The difficulty could be endless - in that you could run into an area that is completely off the grid. An area that blocks any wireless signals. Enemies that have their own wireless cybernetics designed specifically to not only interrupt yours, but also hack yours. *Any good cybernetic wireless piece is going to have its own firewall, unless you're willing to sacrifice it in order to push your processing power (Distance to target, speed of hack etc.)
I would rather see that because it has some imagination to it - but from what I've seen, it doesnt look bad. Just less... "role play"ish.