AFAIK, when you download the game from any site except Steam, you download an image of what is on the distribution DVD. Just as with the DVD, you can install it, re-install it, and modify any and all files, including the sh5.exe.
When you buy from Steam, you accept their terms and conditions, which include a DRM scheme which does not allow you access to the sh5.exe. That file is created at runtime from a compressed and encrypted file. The file is erased when the game exits. Any attempt to mess with this process might get you on Steam's Bad Actor list, which anecdotally appears to be a one-way trip.
Getting a game from Steam is analogous to leasing a car. You have constructive use of it, but do not actually own it. The .exe file is released to you when you need it, but isn't yours to modify. As with leasing a car, this approach works great for some people, and is unsatisfactory for others. YMMV.
For the official patch files, run Silent Hunter 5/Support/GameUpdater/gu.exe
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