It's established in Batman #655 that Alfred is in charge of tending to the needs of the bats in the roof of the Batcave.
Since it's a heavy part of the established canon that "The Batcave contains bats" (along with "Bruce's parents are dead" and "Bruce Wayne is Batman") I think we can reasonably assume that the Batcave in the Nolan trilogies is similarly bat friendly.
Purely FYI: The DC Visual dictionary notes that the bats in question are American Brown Bats
"though the scores of American Brown Bats (Myotis lucifugus) perched high above the Batcave floor were a nuisance to Alfred's fastidious cleaning..."