Well, a bit of progress. I create groups of lighthouses in circle 1km and disable them exept one. Disabled all lighthouses from west coast of America.
Next i disabled all river lights, lights in big bays and deep firths. Number of lighthouses by this method was reduced to 10710. At morning will continue to do one lighthouse per port and sort for lighthouses, lightboats and buoys.
Result visible here:
http://www.ucw.cz/~jerome/lighthouses.html (be patient, table is realy huge)