Technically there is no HBM1 and HBM2 in the JEDEC spec. The only reason it exists is for SK Hynix to ramp up the technology faster. It's easier for them to make HBM1 with constrained operating parameters. You are correct that HBM1 is only limited by the number of vertical stacks. The total number of stacks on the interposer isn't limited. It would make the interposer more complex. It's currently being fabbed @ UMC @ 65nm to keep costs down.
I'm not sure why people keep pushing the idea of a hybrid HBM + DDR setup. That resurrects huge negatives that HBM eliminated. Your GPU would have to have PHY for the HBM and have a memory controller for the DDR. HBM moved the logic slice into each HBM interposer stack thus saving GPU die area and complexity. HBM saves a lot of power by going wide and slow. You'd be going backwards by using DDR. Also, system memory is already your second slower pool for a GPU.
Edit:grammar
Nintendo traditionally doesn't take many risks with hardware. They use older IP / tech at discounted prices so they can profit off the console sales. That being said I'm guessing they will change course due to the failure of the Wii-U but they're still a conservative company.
For these reasons I doubt Nintendo will be going with a HBM design unless it's more cost efficient and yields are at acceptable levels, something that may be a reality if this thing launches in a few years but not if it's (rumoured) to release early next year.
I agree a hybrid solution with HBM doesn't make a ton of sense as it would just add too much cost / power usage.
Nintendo will likely take the safest most available and cheapest X86 hardware option that can still compete with Xbox One and PS4, to expect them to really put out anything better is wishful thinking.
High bandwidth low power DDR4 (my guess is 6-8GB if or when DDR4 hits peak production) attached to an APU with latest GCN tech + 4 low powered Carrizo cores would likely be more than enough to compete and still be cheaper to manufacture than the other systems.
If dual channel DDR4 isn't fast enough to feed the APU they can always integrate a triple core memory controller on the APU or go with a small amount (64-128 MB embedded eDRAM) but this is probably unnecessary and would add too much to the cost.
Remember Nintendo has a basic OS on the Wii U that runs on a custom ARM controller that requires only 512MB of system storage and 1GB of RAM. Compared to what Sony or MS offers, this would provide them a much smaller memory footprint unless they really plan on competing with them in media centre space as well (doubtful).
Anyway the Wii-U will likely be the last Nintendo console I buy. I never buy Nintendo consoles for the graphics, it was always about the core games. The new generation of gamers have no real attachments to these older franchises and the gamers who do have mostly moved on to PC gaming or Sony/Microsoft.
Now Nintendo cares more about selling stupid Amiibos to unlock parts of a full priced game where the content already resides on the disc (their version of DLC, although they're getting into that business as well).
Not getting myself or my kids into this trap