Is Uncharted guilty of ludonarrative dissonance?
ND themselves acknowledged it multiple times. As I said, UC4 has a trophy called Ludonarrative dissonance. Bruce Straley himself said that they managed to solve LD present in Uncharted with TLOU.
You are kinda describing it yourself. The game chooses not to acknowledge a major part of what the actual gameplay is. You say that "well, characters just dont care" which would be fine if the game was more cartoony or whatever, but it's very much grounded in reality and human lives are shown to have the same value as in our reality. It's not like there aren't cutscenes where our heroes don't fear for eachothers life or whatever. And, perhaps most importantly, Nathan and co are still ultimately shown in a good light, as the "good guys" despite rampaging through thousands of men. It's not even possible to argue that it's all in self defense because quite often the characters set out to go on a reckless adventure just for some treasure.
On top of that, Nathan's general easy going, jokey, quippy attitude just really clashes with all the murdering and can be seen as jarring. I don't really care about LD, videogames trying to tell a more traditional style story and also having fun gameplay is a difficult thing to pull off without it, but UC is absolutely one of the most egrigious examples of it.
TLOU has almost zero LD because it takes place in a much more hostile, desperate world than ours and you play as a character that is an established killer, and isn't really morally superior to anyone else you meet in the game.
Tomb raider acknowledges the killings, and actively makes them a part of Lara's character development, especially in Shadow. Her paranoia, obsession, self centered attitude all stem from having to defend herself at the start of TR13 and start killing. Again, I can't emphasize it enough: the actual execution of all this isn't the best, the writing is dodgy in all 3 TR games, and not even consistent, but there really isn't much LD outside Lara learning to handle guns like a tier 1 operator within the time spam of 5 minutes due to gameplay reasons i guess.