Update: It seems like I got it working now. I reverted to my old save, edited the ship paths, but instead of using Move It I bulldozed all of the ports and built new ones in their place. Now there's just one outside connection per terminal and as you can see the number of ships is a lot more realistic. I also managed to fit a third cargo terminal in there. To conclude: Never ever ever ever use the Move It mod on seaports.