I think you're looking at it the wrong way, since personally I was taught to believe it doesn't matter if the artist tried to put in those themes or if it's just the audience or the academic person's way of interpreting/analysing it, as long as you include facts.
Let me start by saying, when I wrote the essay about Memento, it became VERY clear to me the film is an analogy to the postmodern world. Living on bits/segments of information. Every essay or book I read about Memento supported that theory. Chuck Palahniuk (author) even wrote a short parody about Memento, making the segments of information receipts of shopping instead of tattoos and polaroid. A clever way of saying this is the postmodern world, the capitalistic world.
Personally, I don't know if Jonah or Chris thought and looked about it this way when writing. But a good film is ambiguous enough for it. It doesn't throw the entire information in your face. It doesn't tell you "ok, right now we'll do this and this and this" like a sort of, silly monologue from a villain right before he thinks he's going to kill the hero.. it shows you things. When you see information rather than being fed it with a spoon, you can translate this information differently. You have more space for it, to put in your own thoughts and ideas. A good film allows you to do this.
For the record, a friend of mine who knows nothing about film wrote her essay on Armageddon. While I found three books and countless essays on Memento to help me, and went very deep into the themes of the film, layer after layer, we didn't find a single essay or book written about Armageddon (I helped her search for it). Her final work was very shallow and on the surface. Even if you try really hard and say 'the meteor in the film is an analogy for the corrupt government'
or something idiotic like that, the scenes are too clear, too obvious, too in-your-face for you to be able to say anything different. I honestly can't find or think of a way to translate that film any differently than what you see on screen. It's too obvious.
Now back to your initial question, whether the visionaries behind the good films actually think of those themes in advance. A film like Tree of Life tries extremely hard (imo, too much) to be symbolic. If Armageddon tries hard to escape symbolism and ambiguity, Tree of Life tries all it can to say "look at me, I have so much under the surface" that the surface itself is shallow and empty (and btw, I did enjoy the film, I think Malick is a genius, albeit pretentious). I do think Nolan, as someone who studied English literature and is clearly aware of symbolism as you can see from names he uses in his films alone, tries to say so much more (almost all names from Inception, Miranda in TDKR..) than what is actually on the surface. A smart filmmaker would have knowledge beyond filmmaking and use it in his films. In symbolism, in dialogue, in everything, to make you think. I have no doubt many of the themes in Nolan's films were put there on purpose. Again, not everything, and in a way it doesn't matter at all, as I said in the above paragraph. Once you put your heart into symbolism and ambiguity, there would be, by definite, countless other ways to analyse your film, ways maybe you didn't even think about. I dunno if Memento was meant to be an analogy of the postmodern world, I believe so because the Nolan brothers are extremely smart and this one theme was very clear and not that deep under surface (plus they've mentioned it in the same sentence as The Matrix before, one film with a similar theme), but I do think that the symbolism and ambiguity they did use on purpose is the cause of why the film can be interpreted in this manner, and so many others.
Hope that makes sense