I can't speak about the HT situation (other than the OS should handle all affinities) but with a 4 core CPU you should be able to use 2 to 3 extra rendering threads + the MTVU option.
Playing with the number of extra threads is needed when some situations in your game tax the GS a lot.
If it's a purely GS limited game, disable MTVU and free a whole extra core for GSdx.

Good news. Again Xenosaga.

First, with 3 Extra Threads, i manage to get constant 60 FPS in cutscenes in Xenosaga III

Second, in Xenosaga I, i tired to use Software Mode while using the A.G.W.S. a known Hardware Mode slowdown cause. Well, here too, with 3 Extra Threads, all goes smoothly @60 FPS.

As soon as i can i will experiment try with other known games that have problems in hardware mode (Silent Hill for example).