Lets put it this way: Flood is like a top and bottom row shield, sort of. When they attack, they become non-immaterial, which is why the shields affect them, so when they do that, they drown.
But yeah, while I don't want them to affect immaterial creatures, it does make more sense if they do affect them. In the Elements 1.21 thread, BluePriest brought up the point that immaterial creatures are affected by all permanent cards, which is true.