The 3DS Virtual Console has been dead for over a year now. I figure Nintendo plans on absorbing the Wii U's Virtual Console into the NX which is why they've given it so much more attention. Right now they have to make separate emulators for home console and handheld, but if the NX portable and home console will be sharing an OS, they're probably aiming for Cross Platform Virtual Console support as well.
So if the Wii U emulators are going to be what the NX versions are based off of, it makes sense to drop the 3DS like they have since it's cheaper then making a bunch of emulators they'll just end up throwing away after this gen anyway. I wouldn't be surprised of that's the real reason GBA and DS games aren't available on the 3DS either.