According to the official 3DS hardware page, the aqua blue color of the Nintendo 3DS will be discontinued soon, but other colors like the Cosmo Black, Flare Red, Misty Pink, Cobalt Blue and Ice White will still be available. No exact reason was released as to why they’re getting rid of the aqua blue SKU.
While this is awful news if you like the color, you will still have some time to pick one up. Just make sure to do so before it’s too late.