Boat are not like cars which always have headlights operated by the driver, which is the case for the boats noted.
However, if we remove the drivers user action to switch on lights it breaks the navigation (anti-collision) lights completely. This is an Arma bug.
Boats 3 and 4 (Shantou) have a large Commander controlled Searchlight.
Boat 5 (PTF Nasty) has dual side mounted search lights operated by gunners in those positions.
All boats additionally have spot lights on each weapon, all controlled individually at the discretion of the gunners.