Is there any game with a GOOD hacking mini-game?
1. Deus Ex Human Revolution/Mankind Divided - It's overused and hacking is overly incentivized by the terrible XP system in the Nu Deus Ex games, but the minigame itself is legitimately good. It's abstract stealth gameplay in microcosm, focused on capturing territory and avoiding/responding to detection. It's strategic, but the random element makes it dynamic, with influence from character statistics and consumable resources (Mankind Divided adds a lot here, plus more hazards in the grids as well). It's also well-integrated into gameplay at large, as it occurs in real time and failing it can set off alarms.
2. E.Y.E. Divine Cybermancy - Basically a stripped-down Final Fantasy ATB system as a hacking minigame. Keep your attack and defense high while weakening your opponent and whittling down their Cyber HP before they wipe out yours. From my limited experience there are some dominant strategies that hamper its depth, but it's engaging enough and, like Deus Ex, it occurs in real time and is influenced by your character statistics. It's also pretty fleshed out in terms of what can be hacked (remotely, I might add) and what actions can be performed by doing so.
3. Paradroid - I haven't played it myself, but am aware of it because it's one of the first hacking minigames ever and was copied wholesale in Neocron. You have to place charges along circuits to fill up or contest as many of the nodes in the middle as possible while your opponent tries to do the same. Each side has a limited number of charges that must be placed before the timer runs out, and each hacking grid will have junctions and switches that require quick reads. Again, a mix of strategy and dynamism. In Paradroid the number of charges is determined by the difficulty of the hack and is a central part of the challenge; in Neocron it's affected by character statistics.
4. System Shock 2 - While the hacking minigame on its own offers little beyond clicking nodes and praying for RNG (you can decide to risk breaking the device by clicking red nodes but it's usually ill-advised), the hacking minigame gains a lot from its implementation into gameplay at large. It occurs in real time so the player is vulnerable while doing it, it's affected by multiple character statistics, and comes with a resource cost that imposes risk management. By contrast, Bioshock's minigame requires more input on its own but is also extremely tedious and disruptive to gameplay, rather than complementing it.
5. Nier: Automata - Another one I haven't played, but it looks like a solid if simple bullet hell exercise. That's a good enough formula for entire arcade games and it looks like it has a bunch of unique challenges built for it, plus it's a natural fit with the bullet hell sequences already present throughout the game. From what I can see, hacking supplements your other options in combat and there's some itemization related to it.
In the best case scenario, a hacking minigame should present a contained challenge that has some depth (or is at least not terribly intrusive) and mesh cleanly with other aspects of gameplay, such as occuring in real time, being influenced by character statistics and/or resources, and opening up new interactivity for the player on success or fail. In terms of the minigame itself, the better ones require strategic adaption to variable components of challenge (e.g. different grid layouts) and pit the player against a simulated opponent or at least introduce randomness to create uncertainty and prevent the minigame from becoming a static puzzle. Prey's minigame utterly lacks any of this, amounting to a limited set of Pac-Man mazes without the ghosts. It occurs in a modal interface while the game is paused, with character statistics only affecting the ability to enter the minigame, and most hacking opportunities producing mundane results. It's a perfect storm for an incredibly boring hacking minigame.