I wouldn't say it's a no-no, just that it's not explicitly supported by RAW. They made a conscious decision to treat gems just like currency for the sake of convenience. A Haggling system can easily be turned into a variation of a trade skill, which 4E got rid of by default. Adventurers are professional adventurers, it's what they do for a living. However, as DM you can do what you want.
First of all, is this a kind of interaction your players want? I was disappointed every time I found a gem as a player because I knew it meant tedious searching for a buyer and haggling on a price. It wasn't fun to me, but it might be to someone else. Honestly, if the players don't like that kind of thing, I'd just skip it. As DM, you might feel that it's too gamist, but sometimes trying to make everything realistic can bog down a game and make simple things like shopping a real chore.
Make sure you find a solution that's fun for your group, whether it's following RAW or making up your own thing. Having fun is more important than RAW or realism.
And who nows, maybe every emerald in the world just happens to naturally occur at the same value.

There's nothing to stop you from even changing up the values of the gems to the normal amount they would get in treasure, but I wouldn't really make them haggle to sell them or get them appraised. Looting and appraising are parts Adventurer's skill set.