Mr. Bennet has said that signs is a non-existentialist film. However, that statement, like the whole issue of religion, is subjective.
In the film, Graham suffers the loss of his wife becuase a very overworked doctor falls asleep behind the wheel. After her death, Graham loses his faith becuase of the absurdity of the event. When the aliens come, it is not a prayer to Jesus that keeps the aliens from killing the Hess family, but boards and nails. The news report after the attack ends states something about middle eastern cities. Incidentally, this was where gun powder was invented, again, save yourself. The alien that almost kills Morgan is only defeated when Merril "swings away" with his record setting baseball bat. The aliens do not attack with magical super inventions, but with some sort of simple poison, they can not regenerate lost limbs, or do anything miraculous. They have a hard time with turning door knobs (for God's sake). The water spilling to kill the alien was not a literal device, so much as it was a caricature. Set up to poke fun at what religion promises for those that stir trouble, as it appears very silly on a literal level.
To say outright that this was an atheist film would be a stupid thing to say. There is way too much just beneath the surface that supports the idea of a greater being governing the universe, but after a close look at the film it would be unfair to say that there is nothing pro-existential about the movie either. MNS probably intended it that way.