Those holes/depressions are Port Holes. Most of us drill'em out.
Option to to use some Tempra-type paint to fill the holes- them wipe off excess on hull works too. The port holes really stand out with gloss black.
Another option.... I have tried drilling the port holes in another model , painting the hull, then using Testors Crystal Clear in each port hole to simulate glass, and then adding the deck. However, I found this to be awkward as I feared, with good reason, scratching or marring the painting on the hull while getting the deck glued in place. I just drill now.
Glad you spotted the locations for the Torpedo net booms
You can make your own Torpedo net to be rolled up against the hull. I read of one modeler using thin black shoe lace.
To show the net extended there is some PE out there to show it hung in place but it is sized for a water-line display.
I have not built the Dreadnought but I am interested in getting the Trumpeter kit as I consider it better than the Zvezda version.
Thanks for starting this thread. Sign me up for the duration.
Nino