If i remeber correctly even in standard game there are coast(aka ocean) tiles and lake tiles and having a coast tile is requirement for any ship or ship building. That this is intentional is indicated by coast giving +1food+1gold, while lakes give +2 food and +1 gold (both in faerun and in standard). So the lake tiles have already the lighthouse bonus included. For standard games this makes lake as good as coast, as standard coast does not receive any further bonus. Traderoute link requires even in standard game an explored unbroken chain of coast or ocean tiles between the two cities with harbor. Therefore a harbor on an enclosed lake cannot give traderoute anywhere. (maybe to another city on the same lake, which also has a harbor modded, but it might be that lake tiles are generally not counted as traderoute). You see this tw nicely when some enemy ships are along the explored route, the traderouteicons of the cities show the traderoute is broken. The game bonuses also change accordingly (e.g. i had a standard game, where i finished liberty tree and got +1 happy per traderoute, whenever an enemy ship blocked some routes happiness went down accordingly).