My scanner does that too, as shown by the darker 
cels on my site. :P I've found recently that 
changing the setting for what kind of image is 
scanned helps a lot even though it takes longer. 
(Switching from "photo" to "illustration: art 
book" for example.)

As for ethical scanning issues, I tend to follow 
the same guidelines for cel scans that I do for 
photo scans. I generally touch up the color 
balance and remove dust and scratches from 
scanning, but the goal is to make the image look 
as close to the original cel as possible.

Anyway, just my two cents for an interesting 
topic. ^_~`
-Snake-