It kinda defeats the purpose of "limited edition" if you unlimit them so I seriously doubt they will go ahead with an exact replica of the initial release but might do another similar release. Besides the 3ds new has removable covers anyways so it is really easy (and cheap) to get custom snap on...
While they really bungled this up making so few that also increases their collectability. Either way it wouldn't be fair at all to those that already set aside time on release to preorder or got into bidding wars on ebay for them to suddenly water down the market now. If you are smart and wait...