CL40 is better than CL46. CL stands for CAS Latency, or Column Access Strobe Latency: lower is better.
That being said, I have yet to see any head-to-head comparison between 5600 CL46 and 5600 CL40 kits. My assumption is that it would be minor in most cases. The primary performance benefit to higher-frequency (and therefore higher-bandwidth) RAM is iGPU performance. I wouldn't expect that to be terribly latency-sensitive.