Don't quite understand the question but this looks like the stock game to me.
You can only 'see' ships on the Nav.map when your crew see's the ship(s) otherwise its just a contact report given to you by..... someone
to make it easier to find targets.
When you have contact reports turned on in the game options you'll see those markers popup for a short time on the Nav.Map (but
only as contact report), zooming in on them will not show you the vessel.
When you click on that icon you'll get a message saying something like:
Merchant, heading S, medium speed. Draw a line from the vessel down south and if you're close enough calculate a intercept course.
PS_ The big square things are convoy's... the bigger the square the larger the convoy
.