This particular clip is what convinced me to get into the game (potential spoiler) [0].
Almost all the areas have Nakatomi spaces but it is entirely possible to never use them. Likewise one can use them almost exclusively.
Unlike Human Rebolution where these spaces are occasional treats sprinkled out by the devs, they are more properly "worked in" in Mankind Divided.
My point for it being a shallow imitation should be reserved only for the plot and themes of the original game, which are far more subversive and interesting than the ones in MD or HR. But I do agree, gameplay wise Mankind Divided is very well done and does fit the Nakatomi Space paradigm.
There are few games that fall truly in that genre, which is a shame as (to me at least) it’s the video game genre that is most interesting from an “interactive medium” pov.
Arkane games (Dishonored, Deathloop) have some segments that get close, but at their core the games still have a few privileged paths (and are about killing people).
One fun indie game that uses a voxel engine effectively for open ended gameplay is Teardown (and it’s not about killing people!). The maps are quite small though. It’ll be exciting in a decade or so when we can run such engines at much higher dimensions.
I would recommend Streets of Rogue from the indie sphere. It doesn't have vents you can crawl through but you can poison the ventilation system, bribe the police, hack security robots, hire people as bodyguard or to cause a ruckus. Surprisng amount of options for a top down roguelike.
Deus Ex, Thief 1+2, Dishonored 1/2/Death of the Outsider, Prey 2017, Bioshock
Ones I've heard great things about:
System Shock 2, Arx Fatalis, Stalker
The least old one is 9 years old though, and thief 3 is like 20 years old.
Most people hate those with a passion, and only recommend Thief 1 + 2.
Never played 2 but always hear it is amazing.