Yes you can add these ships to ports through the mission editor
Quick lesson if you have never used it:
Open the mission editor in the SilentHunterIII folder and click on the file top right then select new
You should then have a map with nothing on, zoom in and move with the hand icon till you get to where you want to go - we will use Kiel
When you zoom in close enough to the port use the menu buttons on the right - select Sea then the country you put the ships in then roster
Scroll down to the ship you want and drag the name onto the map where you want
You are then faced with this screen
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Make any changes you want - the one on screen is for a docked ship with ammunition cargo - when you have made your changes Accept and your map now looks like this
Now go back to File - top right and scroll down to save scripted layer as
give it a name different to the one you are using such as trial - congratulations you have now added a docked ship
If you go to C:\Program Files\Ubisoft\SilentHunterIII\data\Campaigns\Campa ign and open the file you just created with notepad
you will see you have started your own .scr layer