Some of the earlier versions of V1's even came with stickers so you could decorate the toy yourself as they had a plain shell!
If you are going to put a sticker on a highly decorated one,though, it may take off the paint when you remove the stickers. The paint on tamagotchi's appears to be quite soft and I have found that it wears away with use anyway- especially around the buttons.
You are pretty unlikely to find any 'used' tamagotchi that doesn't have some paint damage- so if you want to use stickers- I wouldn't worry too much about the paintwork!