This should not affect throughput, but rather affect random IOps, especially random read IOps is affected by CPU performance.
Note that on Windows platforms, the I/O backend is single threaded, meaning it makes use of one core only. That means on quadcores with hyperthreading, you can be 100% CPU-capped with a cpu usage of just 12.5%. Keep this in mind and do more thorough benchmarks.
Note that disabling C1E may not be wise, since the benchmark does not combine the I/O with heavy CPU usage, like is expected in a real situation. So you may not really gain anything other than more reliable benchmark results by disabling C1E and other important power saving techniques.