Game just worked out of the box, no crashes or graphical glitches. But is pretty old, so first thing I did is to install "resolutionfix" mod. Dropped the downloaded files to the game directory. Made some changes to the "d3d9.cfg" file. ( Changed resolution to their respective values, 1920 x 1080 in my case). Also modified the "main.cfg" file in "game directory"/SH3/data/cfg/. This changes fixed the resolution.

Next I got "always game paused" error. Apparently this one emerges because of missing "main.cfg" (same one that was mentioned earlier) that should have resided in C:/Users/"username"/Documents folder if it was a Windows installation. What I did is to copy the earlier mentioned main.cfg file to the same SH3 directory and all of its subdirectories. And then copy the SH3 to the "/home/username/.var/app/com.valvesoftware.Steam/.local/share/Steam/steamapps/common/Silent Hunter 3/SH3/data/cfg" directory. This one was the hardest part to figure out and took me a day.