Well for one thing, this ending is abrupt as all get out. And still, we're ready for it. Poe sets it up with a sharp contrast. The old men look forward to whatever comes next, as our narrator tells us, "here is upon their countenances an expression more of the eagerness of hope than of the apathy of despair" (26), while the narrator is scared out of his wits, he promises: "to conceive the horror of my sensations is, I presume, utterly impossible" (25). He does muster a tiny bit of curiosity about their destination, which he frames in terms of scientific discovery, but that just sets him up for the final horror as the ship tumbles into the whirlpool like so much whatever down a drain.
That last bit is important, because what Poe doesn't say in the ending plays a larger role than what he does say. If "MS. Found in a Bottle" is about exploring the unknown—or, more specifically, how the unknown can gobble us up—then he has to leave the narrator's final fate up in the air.
The ship could get sucked to the bottom, it could move on to another plane of existence, or it could get sucked through the center of the Earth and pop out in the North Pole (the best option, if you ask Shmoop, because hello? Santa?). We don't know because Poe doesn't telling us, the jerk. And by refusing to tell us, he lets our imaginations play with all the horrible possibilities. That's a time-honored way to scare the bejesus out of the readers, as well as stressing the story's overall notion that some parts of the universe aren't meant to be explored, thank you very much.