I was referring to two different options. USB over Lightning is one option.
As another, more hackish option the board surely has some SPI pins.
That said, because it is software-defined AND you have root, *perhaps* you could do SPI over Lightning. That's not what I was suggesting, though.
At first glance, I would guess that Lightning is done over GPIO pins (with maybe some DMA thrown in), rather than a specific ARM "peripheral". But, since Apple actually rolls-their-own ARM designs; it would be logical to assume that they DO have some sort of custom Lightning i/f built into their SoCs.
They might talk to their radios, gyros, etc. over SPI (and/or I2C); but, in such a tightly-integrated device, it might be pretty hard to come up with an "enable" pin for your particular, non-planned-for SPI device.
Personally, if I was just using it for some "offline" storage that didn't require "Always there" access, I'd just use a Lightning-based Reader/Writer (Amazon has a nice one for SD and MicroSD (albeit a little pricey) I've been thinking of getting), and something like the GoodReader App, to access the SD storage and the "local" files. Life's just too short to ass-around with jailbreaking to get access to a POSSIBLE SPI i/f. And then you have to write some sort of Driver, and then you have to figure out how to expose access to that Driver, etc. etc. By the time you get THAT familiar with the innards of both the Device AND the OS, you'd mightaswell be making money with those skills... ;-)