The GPU clock is actually fine. Dolphin won't push it as far as PC games will unless you really crank up your graphical settings. However, Wind Waker isn't very demanding on the GPU, so 540MHz is okay.
What does look like a problem is that the game is running in Interpreter mode. This is very slow and should not be used for daily gameplay. Click the Config button and make sure you're using the JIT recompiler. The JIT recompiler does fall back into Interpreter mode for some instructions, so this may be a false positive. Still, double-check; JIT recompiler not Interpreter.
What does look like a problem is that the game is running in Interpreter mode. This is very slow and should not be used for daily gameplay. Click the Config button and make sure you're using the JIT recompiler. The JIT recompiler does fall back into Interpreter mode for some instructions, so this may be a false positive. Still, double-check; JIT recompiler not Interpreter.