Okay, my theory why the /S is better than the /H:
Ayrton Senna was much more revered in Japan for his world titles for Honda in 1988, 1990, and 1991. Damon Hill hadn't yet (as of 1994) achieved the same level of supporet from the fans.
At places like Suzuka, where the Japanese GP was held, it was also a Honda testing ground, and a factory town. Senna was pretty much a local god for affirming Honda's place on the world map. In a way, having Senna win all over the world, justifies the sale of cars all over the world.
So, the /S was crafted better by the PD programmers because of this. Also, they put the /S as a prize for winning the second-longes race series, designed for the "hardcore GT fan", not to mention the completion of the game.
The F094/S is to GT3 what the Suzuki Escudo is to GT2, and what the FTO LM was to the original GT.