The holes are punched in the cels before they're 
painted, because the image needs to be registered 
with the other cels of the sequence/layers.  I 
really don't know how the xerox process works 
with cels, but when I did animation we'd place 
the drawing with the holes on a pegbar, then 
place the punched cel on top of it, also using 
the pegbar, and then trace the image.  That way 
the cel is perfectly registered from the start.

As far as I understand, the backgrounds don't 
have them because floating peg bars are placed 
over them on the animation stand when they're 
being filmed, and thus kept in registration that 
way.  Dunno... I'm probably wrong, I never had to 
use one.

Cels are sold punched and unpunched, because 
they're cheaper unpunched and so some studios 
prefer to do that themselves.  The standard 
animation hole punchers can cost a lot of money 
(something I still can't figure out), plus it 
takes a good deal of time to punch cels (trust 
me...).  So, it's cost versus manpower, I suppose.