There are two Lighthouses in the Iki Island Expansion for Ghost of Tsushima: Director’s Cut. These are completely optional and are not needed for a Trophy. These will also offer a minor Legend increase to Jin.
Yahata Lighthouse - North of Iki Island
This is a simple one to locate, simply make your way north from Fort Sakai to the coast, you can’t miss this Lighthouse. Once you reach it, head to the left side of the Lighthouse to find a path leading up to it.
Thieves Rest Lighthouse - East of Thieves Rest Village
Another Lighthouse that is simple to locate, make your way to the Thieves Rest Village found to the east of Iki Island and then continue to head east to reach the Lighthouse. This Lighthouse is occupied by Mongols, so you’ll need to dispatch them first before climbing the ladders inside to light it.