Hmmm... I didn't notice that, but SSS is actually a problem one because on real hardware it sometimes fails to play samples when a song gets started. I'm still learning how to make smooth HES hacks on games that use samples.
edit: I just compared Super Star Soldier on HuCard (on my CoreGrafx) and my HES Visual version, and both have identical-sounding samples (ie: sounding really nice). The only change I made was increasing the global balance (to $FF) because the original HuCard tunes are too quiet.