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.

For a researcher who's both familiar and happy with Cocoa, I assume jailbreaking wouldn't be a big hurdle.

Hell, GNUStep was created just to port a single application!