There can be all sorts of issues. Two of the most common are having Silent Hunter installed in the "Program Files (x86)" folder, where Windows will prevent any modding from occurring, and rollback your changes, resulting in a partial mod activation. The 2nd thing is if you use Windows archive manager to unzip your mod download, you end up with a double folder, and when you go to activate, the mod never makes it to the correct place in the game files. If you open your game folder, and find a folder with the name of the mod in the same location as the Data folder, that is what has happened. In the MODS folder under your Silent Hunter III install, open the "ModName" folder (whatever your mod's name is), and if you find another "ModName" folder inside, you'll need to drag that folder out from inside the first folder, which means you'll have to go somewhere else with it temporarily, delete the now empty "ModName" folder in the MODS folder, and then drag the real "ModName" folder with the "Data" and "Support", etc. folders in it back into the MODS folder. It's a lot easier than it sounds...
If your game is installed in the "Program Files (x86) folder, post back with which Silent Hunter III you have (Amazon download, Steam download, old disk, newer disk, etc), which OS you are using (Windows 7, Windows 10, etc) and someone can help you out.