Yes, Dolphin does have lots of desync issues. They are less worse if you disable Dual-Core mode (that's the reason only SC mode is kinda supported when using netplay). But even with SC, unless you run at full FPS all the time you'll run into problems (yes, 95% is still not good enough!).
The issue is unlikely to get resolved anytime soon because a proper synch mechanism (if you can even define "proper synch" properly) would probably defeat the purpose of Dual Core mode, i.e. speeding up stuff.
The issue is unlikely to get resolved anytime soon because a proper synch mechanism (if you can even define "proper synch" properly) would probably defeat the purpose of Dual Core mode, i.e. speeding up stuff.