Wholesale memory cards are dirt cheap, even into the 64GB size range, and that's when buying them through 3rd-party companies.  3DS carts suffered from still being tethered to a ROM solution for the purpose of DS backwards compatibility, but even ROM pricing has gotten cheaper since the glory days of carts.  ROM suffers most from capacity limitations, so you stop using ROMs and use write-restricted NAND RAM chips, instead.
Given the volume that a company like Nintendo would need to buy and the kind of contract negotiations they can leverage, I think it's safe to say that there's not much to be concerned about price-wise in getting a write-protected NAND RAM cartridge that matches Blu-Ray capacity while also providing the added benefit of faster load times across all devices in the NX ecosystem.
Again, it will still be more expensive than a disc, but not the astronomical cost that you think it is.