Mods work with steam, though it's a bit tricky to set up.
On my computer anyways, you need to install JSGME into:
C:\Program Files (x86)\Steam\SteamApps\Common\Silent Hunters Wolves of the Pacific
And yes, get the U-boat missions version, it adds fixes that you will probably need for most mods. Even if you're not interested in the U-Boat stuff
