First, just wanted to point out that Night seems to have some issues with water. I seem to recall a scene in Sixth Sense where a character freaks out over a spilled glass of water, the hero's one vulnerabilty in Unbreakable was water, there is the water as a poison in this movie, and now Lady in the Water. I don't recall a water element in The Village, however.
Anyway, I found some of this interview useful. I think Night thinks alergy to water is no more or less silly than the common cold virus killing aliens in War of the Worlds, and that the movie really was more about faith than aliens to him.
From the Sci-Fi Weekly Interview:
Sci-Fi Weekly: At one point in this movie, Joaquin Phoenix said it's like War of the Worlds. Is this your intelligent version of it?
Shyamalan: I'd say so. It wasn't like, let me do ... my version of it. ... I keep in mind ... that Orson Welles radio play. To see this woman doing the dishes and stopping the dishes, and she has that little apron and wipes her hands on the apron, and she comes towards the radio. And then that pang, what she feels: That's what I wanted to make the movie about. That pang. And it seemed like in this day and age, with the media ... you instantly know everything about everything. And so what a great time to do this. You know what I mean? "This is happening in Mexico. This is happening in India." And this little family in Pennsylvania has experienced something like that, trying to connect everything.
Sci-Fi Weekly: This movie, like your other films, deals with faith.
Shyamalan: I guess I just keep pounding away at this until I get it myself. Which is kind of a guy waking up to his potential and who he is and the things around him. So all three of those movies are this guy waking up. I don't know why, I just keep writing that guy. I could easily write another one about a guy waking up and realizing this. And then the supernatural or the sci-fi elements of the movie—the ghosts or the aliens—is kind of irrelevant to me. It's just a backdrop.
A man learning to believe again, ... believe in himself in Unbreakable. Believe in love in Sixth Sense and believe in himself as a therapist in Sixth Sense, in his job. These are the things that I was dealing with at the time. Each one is a different thing. And in Signs, it's basically this faith, believing in fate. Believing that ... [as] Joseph Campbell [said], "Take the adventure that's being offered to you. ... There will be guides to help you along the way, and if you refuse it, you will experience a negative adventure in the same way through your life." And in a way, that totally connects with me, that those guides he's talking about. ... It's there if you choose to see it.