USB 2.0/3.0 vs Soundcard Line in & S/PDIF

Which interface use less CPU resource and latency?

Jim's right: the differences are not great enough to be the deciding factor in choosing your hardware and recording methods.

But to answer the question, there is a small amount of additional overhead for USB. But don't worry about that. Choose your interface based on features and reputation, not how it communicates with your computer.