The cables are not usually covered...but they're only like $20 and easy to replace.
I know it kinda sucks having to pay replace something after you just put down a ton of cash for it, but let me re-assure you that Hobie has, by far, the best warrenty/customer service in the business.
And also if you havnt' already, check out:
http://www.hobiecat.com/forums/
and scroll down to the kayak fishing area...tons of good info there on drive care and adjustment, new heavier duty parts available, and lube tests/selection....along with all the other public forum BS. A very cool site!!