Yep
As long as your iTunes library on your computer is mapped to the external HD connected to the Airport Extreme (meaning you can see and play the files in iTunes), it should work just fine.
Remember, the ?TV SYNCS content, so as long as it's on the network and properly accessible through iTunes, I don't see why this would be an issue. Sure, it might take a bit longer to sync, but in actual use the difference shouldn't matter.