I haven't played the first deus ex, but in HR and MD stealth is the only viable option, shooting is shit. Dishonored has the same concept: you are supposed to play it stealthy. I don't remember any game where you have both options and stealth is more difficult (it doesn't mean they exist, probably just my ignorance)I mean games where stealth is a truly viable option, like Deus Ex, Dishonored and the like.
Ideally, though, as a game designer you want to make sure players don't get screwed because they missed a couple terminals they could have hacked in one mission - because there are no "radiant" style missions where you can just grind out XP, you kinda need to make sure players have a chance later on in the game. I think that's the philosophy behind end-of-mission quest rewards. It sooort of keeps everyone on a similar playing field, even if players have the opportunity to earn more (or less) XP than the average due to missing/not missing various xp-giving actions.
Yeah, of course it can make sense from a game designer point of view (and obviously I'm not, so they know better), but once you decide to limit exp to skills and not "numbers" (HP, damage output), in action RPGs you don't really have the problem of that kind of progression. Decide fixed numbers and you'll need to balance the game only once, not caring about the level the player is supposed to be at that point of the game. Thinking "cyberpunk", give me eddies at the end of main missions and I'll use those to buy cyberware and weapons so I'll get stronger and you, as a game designer, can keep track of what I'm doing. Street creds will limit my mission progression and cyberware options since they limit contractors and vendors. The game designer knows exactly how "strong" I am: given a fixed number of eddies, I must decide which cyberware to buy, exactly like unlocking and equipping skills in TW3, but without breaking immersion, since it makes sense that cyberware brings different perks. I mean, it's the same as XP, why do you need both? Because we're used to it?
But that's just talking for possible future games, since the traditional level system has been already confirmed for CP2077.