Well, you know, covering an exhaust port makes it, like, really hard for the exhaust to, well, get out ...
...and things, like a proton torpedoe, to get in. The Empire was supposed to be all evil and whatnot, right, so they should've just put exhaust port inside the Stormtroopers training facility, or some such place.
But that would kill the Stormtroopers, who are needed to fight!