The thing is, they just act as Backround support. They just kinda are THERE, and there's lots of field agents you see doing nothing because they work as supporting cast in said books.
So either SHIELD has entire armies of field agents to do literally nothing or they actually are doing their job quietly and efficiently away from superheroes.
SHIELD has always been involved in superhero stuff (Steranko's Fury, Captain America's comic, Iron Man's really early stuff, etc) but they don't exist to act purely as a bureaucratic support to superheroes; they have actual function that most superheroes don't handle because it's sort of outside of their purview and area of speciality.
Black Widow's basically one of the few exceptions to this of course, because spying was literally her first vocation.