Yes, when there are bright lights ashore, and traffic lights which can be confused with running lights, there can be an issue. I have far more of an issue with tugs and tows, than with another C Dory! I have a lot of experience with back ground lights, with thousands of miles of night sailing all over the world. I have never run deck lights, except on a couple occasions to light up sails, or decks--long before AIS, when I was not sure a large freighter saw my lights. The best light for these conditions is a bright all around light. I always be sure that my "all around steaming light" is as bright as possible. That is the one which is seen first by commercial shipping. A quick flash of a search light (not in the eyes or bridge of the other vessel, is usually all that is necessary. Good that you maintain the night vision.---ambient shore lights should not hinder your night vision, unless you are very close to those lights.
Yes, we have the same problem with search lights on tugs and tows on the ICW--but a call on VHF is far better than deck lights. These boats which are lit up, usually see you on their radar. Squiders on the West coast have these very bright lights also. But there is the occasional sport fisher which runs into a restaurant--and not a not one can do about that, even with all of the lights in the world!