Well I think I have found out what it is. When I placed the player sub in the mission with the Mission Editor I thought I would see what these 2 things did (picture insert).
I haven't done this on any of the other subs I've placed in missions, so when I go in the map screen I zoomed in and when I did a TC I noticed the ghost sub icon appear, if I TC a bit more the icon goes, but as soon as it goes another one appears.
Now also when I first start the mission and press the F12 key I am in Free Camera mode and the sub carries on it's journey, for me to keep up I have to press the arrow keys as you know.
Now if I then press the (.) key it is like the Ship Camera view and it stays with the sub, I can rotate an zoom in the same way as I can on the ship camera.
Feedback appreciated.
Edited to add:
I just tried this on another already scripted mission by altering the sub properties, it didn't work at first but after zooming in and out of the map a few times I got the ghost icon, I could then use the external cam to follow the sub.