According to I, Tyrant, a beholder's body is honeycombed with individual pockets of a helium-like substance called "tiusium" (or something like that - I'm doing this from memory), so one simple sword-thrust into its body doesn't deflate it like a balloon.The Beholder's ability to fly is clearly labeled as extraordinary, and so is not shut off by their anti-magic eye ray. Indeed, they feather fall as an extraordinary effect as well. Apparently their bodies are like helium filled balloons.
Johnathan