If those stickers have little pneumatic cutters on the sticky side that unfold when you stick them on a guitar and cut through the outer side into the mechanics, yes, it probably will have some effect.
obviously don't cover sound holes, but no, won't hurt 'em. I've seen some cool add-ons that way. Two friends of mine have variants on "this Machine Kills/Eats Terrorists" on their guitars (which is a take on Woody Guthrie's "This machine kills facists" sign.) I 'd go for the case anyway.
Actually it will be detrimental to the tone. The guitar makes most of its sound by vibrating the top, if you put a sticker on it its going to dampen that vibration. To a noticeable degree? Who knows, but it will at least a little bit.
Depends on what your guitar's brand and model is... and wether you have a solid or laminate top. And of course it will affect the tone... but it's not going to matter a whole lot if it's not a pre-war Martin, Collings, or something and you record with it... I have a brazillian rosewood D-35 that I'd never do it to, but I painted the Bob Dylan eye logo on my headstock which, obviously, won't affect anything. But of course it's going to affect the value if I ever sell it, but I can always take it off... I didn't clearcoat over or anything.
