I'm not a commercial games composer, but I'd say it really depends on the type of game and the overall sound needed to make that game work. You already mentioned a few (pixel based) games that work well with retro sounds, and then sample quality isn't really a thing (especially if you're just using/emulating old sound chips). A modern looking game will usually require a more modern sound, with more polished samples though. It's just expectations that people will have, based on a game's art style and gameplay, I guess.
But at the end of the day -in my opinion- the samples are just a tool, and it's the composition and arrangement and how you write for/use your samples that will make a big difference. Better samples just make your life easier.