1. i don't think it'll affect the value of the card but it could deter a potential deal the same way you're not really digging the missing cert. at the moment.
2. no, i don't think the seller giving a discount is fair. no one has any motivation to keep the COA without the card. unfortunately, sometimes you just have to take your lumps. sort of like mail that goes missing; it's just part of the hobby.
3. it certainly couldn't hurt.