Technically, yes, but it's infinitely negligible.

It's kind of like taking photos in a museum. One 
instance of flash photography isn't really going 
to hurt anything, but if you have 30,000 people 
taking flash photos every year, and multiply that 
by five, ten years, it's going to harm an object.

So while scanning may expose a cel to bright 
light for a few seconds, it's not as bad as, say, 
hanging a cel in a medium-intensity light source 
for a few years.

-Cres