Most of the hidden stuff actually comes down to exploring rather than following specific story beats. The quest paperchase with all those banking shenanigans, for instance, just needs you to poke around the right spots in town. Something interesting though certain side activities can get locked out if you push too far in the main story, like that whole thing with the missing merchant or the tax collector drama. The quest an unpaid debt is pretty unique, since you'll only stumble on it after breaking out of jail during that stranger in a strange land business.

Your choices definitely matter too whether you spare someone or not can totally change how other quests play out later. The hidden messages stuff is a good example of that. The main thing to keep in mind is exploring thoroughly and wrapping up side activities before hitting those big story moments, especially in places like novigrad where merchants and local politics get pretty tangled up. Nothing's really set in stone quest order wise, but timing can make a difference in what content you can access.