Officially, just the presence of dogs (even on leashes) can scare and change the behavior of ground dwelling birds. Unofficially, if you are going straight for a poo and taking the dog away again, it is going to have substantially less impact on bird behaviour than letting it roam off leash, and / or from end to end of the beach.
But then, can't you train you dog to poo on the boat (noting I'm not a dog owner). Don't get me started on boat cats though. I don't understand that.