Meh, I wouldn't want shows like Daredevil and Jessica Jones being bogged down by having to take Shield into account. It would probably improve the quality of Shield as a show, but I'm scared of the effect it would have on DD/JJ. None of the Netflix shows would be improved by Fitzsimmons being able to turn up, or implementing stuff like the Inhumans into their storylines.
Referencing the biker gang from Shield in Daredevil, or mentioning that one bad guy from Shield on that boxing poster is about as far as you can take it, I think.
It doesn't have to be that, though. Daredevil could have a threat assessment episode where agents manage to corner him, he'd fight back for our viewing pleasure (maybe a baton showdown with Mockingbird, or Daisy messing up his senses with her blasts) and then escapes as Coulson wisely agrees that he's doing good work. Besides, they're here to manage enhanced people, not to deal with the Mafia.
Jessica Jones would have had an encounter with some agents after her public call for witnesses, agents more interested in her own powers than the mythical Killgrave. She'd tell them to f* off in a typical JJ way, and would go her merry way.
As for Agents of Shield, these two would never come to the base, but could cooperate to some extent when a mission brings the agents in Hell's kitchen.