Are real world spies actually known for these things?

Good question (thanks for your post btw. Sorry if my reply seemed a little aggressively sarcastic or repudiative. An interesting question related to complex issues)

I'm not as much of a nerd for this stuff as many

Neither am I, you probably know more than me. There's the odd relevant media though that's pops up occassinally. Intelligence communities reacted publically to recent exposures by whistleblowers, often denigrated as 'conspiracy theorists', vaguely describing their efforts to avoid repeats, what sort of internal safeguards they were putting in place, like who watches the watchmen, internal ideological discipline sorts of things, circling their wagons. There were sometimes internal divisions alluded to, concerning official positions and policies but almost no details given (e.g over surveillance and privacy etc). Some maybe came up around the controversy surrounding actors and actresses illegally accessed nude files.

that's not the impression I get.

That doesn't seem too surprising, there's maybe never been any decent films about espionage or intelligence (Tinker Tailor Soldier Spy is maybe ok). It might be deliberate. Even outdated stuff like Spycatcher is perhaps still controversial (Interestingly co-authored by Greengrass of Bourne fame. Incidentally Bourne is a sort of half subversion of the 'rogue element', being a rogue element of a rogue element). It seems doubtful agencies like their tried and true methods, old operations and modus operandi being advertised, even fictionally. They infiltrated mass media long ago, especially film. It you doubt it, consider the Red Scare. When Russians used it, people liked to call it propaganda (e.g. Alexander Nevsky). There's lots of recent articles to back that up, how groups preserve their image. Film makers tend to shy away from anything too politically sensitive. Maybe that explains why so many conspiracies in modern films are often so ridiculous, if they can't use serious theories, it's what's left. Incidentally, there are some almost ridiculous conspiracies IRL, this film is about a real cartel.

There's definitely a difference between a movie taking a conspiracy theory narrative head-on like JFK or even The Parallax View in a fictionalized example, and movies that simply have stories constructed like/influenced by conspiracy theories.

Very good point. Is there spectrums though? Do serious movies about movies gradually shade into movies featuring or influenced by conspiracy theories?

Lets say films like 'All the President's men', 'JFK', 'The Insider' or 'Kill the Messenger' are serious dramatic ones about conspiracies (it's unclear how the spy or historical drama genres fits in this scheme, but they seem close relations, stuff like Syriana, Argo and Lions for Lambs). What's at the other end of a spectrum? What are the worst offendors? Dramatic films sincerely portraying ridiculous conspiracies (like Interstellar), or undramatic (maybe comedies or fluff entertainment) ones that feature crackpot theories (like the Electronics in Transformers). Is Wag the Dog a serious satire about serious conspiracies, or a comedy? Where does the film 'Conspiracy theory' fit in?