restoring old bike, remove scratched stickers, yes or no?
If you feel the bike has no significant resale value, then why not just do what would produce the results YOU would like the most?

But if you really want to preserve the stickers, but want to avoid the trouble and less than ideal paint job due to masking them, I'm guessing it would be possible to photograph (and PhotoShop) them (or find matching images on the web) and then reproduce them somehow with a reasonably waterproof printing scheme.