SGM You bring up some interesting points!
I would argue that in DX1, the timer is not a gameplay challenge as much as it exists purely for immersion - after all, it's trivial to simply wait and keep hacking and repeat, and in practice the environmental dangers are not really that relevant. I do think there is a worldbuilding factor to it that is appealing, it feels exciting to hack something with a running timer - and in that sense the DX1 approach does work quite nicely.
On the distinction from multitools and lockpicking, I don't think you're wrong here! It does fill essentially the same role, although sometimes I think that's all that is really needed. Using DXHR as a case study, it had the same reasoning when consolidating all 3 mechanics into the exact same mechanic - but even though it's mostly the same mechanically, that has issues both immersion-wise and in terms of making the level design and exploration feel more varied. Or to take an even more extreme example, universal ammo in Invisible War, which made both ammo and inventory management feel a lot more abstracted away from the world.
All that being said, I do agree with your central argument that not everything has to be tied to resource management, and the exact balance here is still something that is being iterated on. To demonstrate this by addressing your concern, the initial idea for more 'trivial' locked computers has been to more commonly tie those to other means of getting into the accounts, such as finding a sysadmin's user account override password, or a database of employee passwords, and so on - but, if this turns out to not be enough, we can easily consider balancing this by for instance only have hacking shards required for the higher security tier of terminal and not the base level one.
Thanks for these thoughts, they are always appreciated! :)