The same thing happened to me a while back. It turned out that my center speaker (5-speaker setup) was messed up. A lot of the sounds in SH3 are out of the center speaker. If you have one, check if it's connected and working properly. If you have 2 speakers, it could be that the game is trying to play sound through the center speaker. I don't know what you could do in that case though.
...Or it could just be a codec...
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