There's currently no game play with hacking. It's a press a button and win mechanic. They should use the defunct Genetic Sampler minigame for hacking any and all electronic systems. Leave the E-Breaches in as a purchasable item as an option for those that are no good at quick time events or who are in a hurry. Accessing sensitive data for download from terminals should also need hacking.
Also give players the option to hack doors rather than having to clone security levels. Purchased E-Breaches could also be used on doors. This would add gameplay and keeps the option for players to use the existing game mechanics of cloning security levels and forcing doors.
Defined by the security level of the door, base or system, repeated failed hacking attempts will set off an alarm. i.e. you want to get into a Level 1 Hab then it gives you ten attempts to hack a system, Level 3 Command in a restricted area gives you three attempts etc.
To tie this into Horizons, hacking Private Data in SRVs could also use the same mechanic of completing a minigame or use E-Breach.