That's still the exception to the rule. You didn't mention the Underdark, and you even talked about NPCs.
Besides, even if "most" underdark creatures had 90 ft or 120 ft darkvision (a claim I find dubious), it still wouldn't mean you couldn't play a sneaky rogue.
Even if you stumble upon a completely darkened outpost manned by Drow (say), and are discovered, you can still hide and do your thing. And I'm saying that as a DM that has run Out of the Abyss.
Anyway, that's a discussion for another topic. You certainly don't have to worry about the 120 ft darkvision of select monsters to choose the Rogue class.
What you do need to worry about (as a DM) is the relative ease with which a group of players can form a darkvision-only party. In other words, the OPs complaint.
Sure there are many ways to ameliorate this. My preferred tweak is to focus on elves (and half-elves) only: to me that's a very simple, very unintrusive tweak that more or less fixes the issue completely
I was responding specifically to your assertion that "ditching torches...(enables) lots of scenarios where the monsters and foes won't see you coming."
The fact is, when their darkvision is twice yours, they
can still see you coming. That doesn't mean they always will, just like when you
are carrying a light source, a sneaky rogue or other character can still sneak up on the outpost. My point is that carrying a light source or not doesn't specifically enable or deny that tactic from either side.
The tactics differ slightly if you are using a light source or not, but darkvision (even a party consisting of all races with darkvision), don't eliminate any particular tactics completely.
The OP is complaining that too many creatures have darkvision and it ruins his sense of atmosphere, and also tactics that are in play without the use of light sources.
Risks of Light Sources: Creatures can see you coming before you can see them. This also applies when not using a light source and the creature have superior darkvision (or other senses). It's easy enough to see that would include Aboleths, angels, behirs, beholders, couatl, death knight, demi-lich, demons, devils, dragons, drow, etc. While a light source acts more as a beacon, drawing attention to you, even without a light source you are at a distinct disadvantage in the Underdark. Clever characters will use the light source exactly as that, a beacon, to mislead and draw attention away from some or all of them. Plus, outdoors is when a light source like that is the most problematic. Underground, with relatively short or windy passages, it's less problematic in terms of being seen at a great distance.
There are also potential issues with fuel and resources, but with multiple spells that provide light, including permanently, it's really a non-issue not because of darkvision but because of magic.
I also feel reading should be more difficult, if not impossible in dim light. Again, dim light in the game is dark enough that it mechanically hinders your Perception. Go outside at late twilight/dusk and especially in the woods. Everything naturally turns grayish. It's much easier to hide from somebody, like when we played Ghost in the Graveyard as kids. That to me is darkvision - low light enough that you have disadvantage on Perception.
Impacts Stealth: The only situation that could be better is a creature with darkvision against a creature without, because they are effectively blind. Otherwise, when in a scenario where everybody has darkvision and there are no light sources, then everybody has disadvantage on Perception checks, which only improves a Stealth opportunities.
Impacts Atmosphere: This is a question of DMing. When descending into Undermountain down the deep well in the Yawning Portal, your eyes (darkvision or not), still need to adjust, beyond that it's just a slightly different description: "As your feet find themselves on firm footing, you're standing in the shaft of light from above, which seems to form a barrier from the civilized world to the inky darkness ahead of you. As you walk farther from that light, it's like being in an endless twilight, a mix of dark and darker, everything a muted gray of one shade or another, until about 20 paces ahead of you is nothing by black, empty darkness." If it were me, I'd still want better light a lot of the time.
The only other argument I've seen is "too many races have darkvision" but the complaints as to why that's a problem seems to fall under one of those three categories. Why do I "need to worry about" this as you say? It sounds like I might "need to worry about" the small number of races that don't have darkvision. Eliminating elves just takes away one possibility (a popular one, of course) but it's still extremely easy to make a party of only races that have darkvision.
The only sort of argument that makes any sense to me is that creatures of the surface (elves) shouldn't be able to see as well underground as those from the Underdark. To start with, they don't because of the superior range of their darkvision (which isn't new either btw, at least back to AD&D). The only solution that really makes sense to me is to differentiate between nightvision and darkvision. That way creatures such as elves (along with nocturnal animals and monsters) still have superior vision in the dark, relative to humans, but it doesn't give them the same advantage underground. I like that approach quite a bit, not because it reduces the ability of elves, but that right now there is nothing that gives nocturnal creatures an advantage. If I'm going to add nightvision, then it's a question of whether I think elves should have darkvision or nightvision. Personally, I don't have an aversion to them having darkvision anyway, so I probably won't change it. But I'll think about it, and probably see what the rest of our group thinks.