Earlier quoted context omitted.
Unless you have a jailbroken device, arbitrary apps you write won't be able to access that stream.
You can use the EAAccessory framework to talk to it. Just use the protocol string "com.southernstars.sw9a". What I'm not sure of is what sorts of apps they'll let into the app store that repurpose the cable. EDIT: Here's my test code thus far: https://github.com/frankus/SkyWireTest
Apps using that won't pass certification, but you're right you can use your own provisioned apps.