FWIW, I have only heard O gauge Fastrack, no S gauge. I would imagine it is all about the same for noise as it's all hollow, hard plastic road bed. The extra 3rd rail may add to the noise level? Some think it is very noisy and some do not notice the noise at all and say it's quiet. Depends on your hearing and we all hear things differently.
If you don't mind more of a 'toy train' look, many have reported using carpet on their layout quiets it down considerably. I really like the O gauge Fastrack. However, due to the noise I went with Atlas which I now like even better than Fastrack and it is very quiet, even on bare plywood. I know you can't get that for S gauge, but if there is a solid rail track available for S gauge I imagine it would be much quieter without having extra sound deadening under it.