If it was that simple they would have done that by now. How long has emunand been around? Even if they did block it in this way, Gateway can just patch emunand firmware to either spoof it's location or remove the check entirely. Gateway gains control over the system via a Process9 exploit in the Arm9 CPU. This CPU is the gatekeeper to the entire system. So they are free to do what ever the hell they want to the emunand firmware. Patching out checks would be easy if you have Arm9 control I'm pretty sure.
Hell, it might not even be possible on a software level to tell if the home menu is being run on system NAND or not. Gateway may have altered code in Arm11 or Arm9 (not sure which handles) to load the system from SD. They can then easily patch it so that when ever emunand home menu or other firmware app tries to check where it's installed, the Arm9/Arm11 cpu (not sure which one handles this) will just give it the physical address it would have had on system nand.
I would bet the reason Gateway pushed out updates to get the last series of firmware updates to work were just related to the cryptography side of things. Before Ultra 3.0, all Gateway users were using emunand on a 4.5 system that has the old encryption keys. So Nintendo just had to employ the newer keys in more parts of the firmware. Boom, emunand doesn't boot. Ultra 3.0 users however are already on the correct encryption keys for the current firmware, So I would bet 9.5 when it drops might actually still boot in emunand. Perhaps the cryptography isn't the only reason. Waiting for Gateway to update to get emunand work again may have been the result of Nintendo already implementing something like this. By default the firmware is supposed to be run from internal NAND. I'm sure there's already checks in the firmware to make sure it's been executed from the right storage locations. Gateway's already patched around that.
Long story short, I don't see Nintendo preventing emunand use anytime soon. Nintendo can only block Gateway working on systems already on a firmware that can't be exploited. Once an Arm11 and then Arm9 exploit is found, all consoles on that firmware is lost to Nintendo forever pretty much. Ultra 3.0 expanded the amount of exploitable consoles ten fold.
Though honestly I think Nintendo is more worried about Sky3DS as that reletively more user friendly and more of the casual gamers (the majority of their market base for this console most likley) would have an easier time picking one up and using it. Gateway requires fiddling around with exploits, setting up emunand, and what not. A lot of these systems are bought for young children and parents probably don't want to mess around with stuff like that. Sky3DS despite it's terrible design and lack of updatability is a bigger threat to Nintendo's profits then Gateway is right now.
Of coarse once they do block it, they'll render all those Sky3DS's really expensive paperweights. I feel sorry for all the people duped into buying one. Hell they won't even make good paper weights. 3DS cartridges are tiny and weigh hardly anything.
I'm betting Nintendo might drop a new SDK version soon though especially with the New3DS finally being available everywhere. Expect to see them roll over to new encryption keys.