For those who struggle with low FPS in Silent Storm, I have found a solution which helped me to fix it. I was using many different guides in the internet (d3d9 was one of the first) and none has improved the performance in Silent Storm for me.

So I found a section about WineD3D on PCgamingWiki
https://www.pcgamingwiki.com/wiki/Silent_Storm#WineD3D

Here's a direct link to solution
https://fdossena.com/?p=wined3d/index.frag

and all you need to do is to download an older version (I used WineD3DForWindows_1.7.51) and extract
libwine.dll, wined3d.dll and d3d9.dll to your game folder.

To improve the performance further, open config.cfg in cfg folder and find next string
"setvar gfx_cl_sky_textures = 4.00"
Change it to "setvar gfx_cl_sky_textures = 1.00", or "setvar gfx_cl_sky_textures = 0.00" if you don't mind a bit worse lightening.