The difference between a theory, a conspiracy theory and the truth are best described by varying levels of evidence. A theory is not currently accepted as the truth, but it might be the truth. A conspiracy theory is something that has been proven to be untrue, but people still believe it and pass it on. The truth is the internally consistent and fact supported state of the world as it was and as it is.
There were many people who were going out on a limb with the assertion that the NSA was probably vacuuming it all up, they had means, motive and opportunity handed to them on a golden platter, on top of that it corresponded with what we would expect to do ourselves when in that position (not that there was any such temptation). The hacker community was well capable of seeing this as a theory, rather than as a conspiracy simply for absence of proof. That didn't stop others from labeling the hacker community as a bunch of conspiracy theorists simply because they could not imagine it to be the truth, but a lack of imagination is not the same as proof and the output of such a process is better described as wishful thinking than rational thought.