Honestly, Hyperthreading shouldn't slow down anything. If so, ALL PC games should show a performance difference, but there's none with Hyperthreading off/on, especially for those with heavily single threaded orientations.
You could try setting the thread affinity for Dolphin in the Task Manager to Core 1, Core 3, Core 5 and Core 7
You could try setting the thread affinity for Dolphin in the Task Manager to Core 1, Core 3, Core 5 and Core 7