I can verify that the GWX Gold supermod installs just fine using the Steam version of SH3, since I did this just last week. My build had the following filepath: X:\Program Files (x86)\Steam\steamapps\common\Silent Hunter 3.
But IIRC if you ask Steam to verify your installation of SH3 after you install a mod, it will naturally interpret this as a defect and try to re-install the vanilla version. So don't do that.
My big complaint with the Steam version so far has been that you need to run Steam first in order to invoke SH3. And when Steam starts SH3, it starts it in vanilla 1024x768 resolution even if you have installed a 1920x1080 resolution mod.
So to get around this I would start Steam by itself. Then I would invoke SH3 separately via the GWX shortcut and then I could play in 1920x1080 resolution ! (Needed to also run the 4GB patch as well)
Later I found a way to cut out the first step. Found out that it was even possible to run this build of SH3 in a completely different folder location.
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