We're talking about fiction. The Reapers could have been anything. They could have been Eldritch Horrors. They could have actually existed before the universe. Looking at fiction the way you do makes me sad.
First of all, that's stupid. Do you think people like Hitler and Stalin never blustered, threatened or talked about things they would do to the rest of the world? Of course they did. It's an effective tactic, instilling fear and breaking the will of your opponent.
Second, why would you use OOC logic in an RPG? That completely negates the point of playing the RPG. You're probably the guy playing D&D and complaining about how your character would have killed the dragon with a rocket.
The reapers would still be a natural intelligence. Chuthulu obviously isn't beyond the realm of human comprehension since we invented the concept of it. There's wonderful speculative science fiction out there that does potray life so alien it's hard for us to wrap our heads around it. But the Reapers aren't that sort of thing. They're perfectly understandable creatures.
The IRL examples are what's stupid. No dictator stands up and says "My regime is beyond your comprehension." Political speeches are used as propaganda tools, sure, and they're filled with jingoism, but they're all about thinly veiled threats. Even ignoring the fact that the major difference between them is that they're actually a risk to occur. Hitler isn't the Red Skull, giving some weird speech to a fire-team he's got tied up in his basement.
In character, Shepard isn't intimidated. Hell, you're locked into saying the Reapers are just machines, and machines can be broken. l'm as unimpressed behind the screen as Shepard was in person.
The point about the OOC line is this: in-setting, the idea of giving a speech like this is moronic. They make fun of it in just about every parody ever - look at Austin Powers, for example. It's not something to be taken seriously.