Sadly the 4 EB Stores I've been to, have taken all Zelda 3DS Consoles off the shelf, resulting in Red,Blue,Black or Pink left. I think it's quite a coincidence that since the Nintendo 3DS Price drop has happened. They're now $194, the Limited edition has now vanished.. Don't forget EB was selling the that edition for $248 around Christmas time, that's $35 more than the standard editions. See here - I made a whole blog post about it.
Search results on EB Games website for "Zelda 3DS"
The Limited edition was seen on the EB Games web store earlier last week, customers were never notified it was a limited time offer. EB Games just don't seem to understand he word 'Limited', for example the White Playstation 3 Limited Edition is still being sold at their stores, so why has the Zelda 3DS vanished?
I personally feel that the limited edition didn't really have much shelf life, maybe in other countries but surely the Australian edition maybe quite rare in the future. Who knows what this means, we might see this back on the shelf if the 3DS ever has a price rise, but I highly doubt it.
eBay stores alike will now be taking advantage of the Limited Edition in Australia. As mentioned before I'm only aware of how Australian stores are, so it maybe still available in the US.