After continuing game it comes out that the deck gun still fully works, I had to use it against another freighter and it worked like a charm when manning the gun and ordering attack by binocular. BTW I play with a Narwhal class sub that has 2 deck guns, forgetting that I did uselessly turn my sub around
After un-manning the gun the red damage mark has disappeared, i guess by manning the gun the crew will do repairs (instead of forming a damage repair crew). That's good to know for the future. Or maybe it was a glitch due to the Narwhal class sub which is a modded sub that is not in the stock game AFAIK, I can't remember wether the stock game has any subs with 2 deck guns, I think not.
XS