Why is Dolphin running slower now?

[Shonumi]

Yes, check the temps while running Dolphin. Idle temps will rarely tell you there's a problem unless your cooling is absolutely terrible (and/or clogged). Dolphin is pretty CPU intensive, so the CPU temps rise significantly when running the emulator.

As for programs, you can use HWMonitor for temps, CPU-Z and GPU-Z for clocks for each respective piece of hardware.