By Sam Dean From the Los Angeles Times San Pedro Bay is looking less crowded these days. The fleet of massive container ships loitering just offshore from the ports of Long Beach and Los Angeles has thinned to 46 boats from its peak of more than 80 in late October. Is that a good sign for Southern California’s congested supply chain, and the breathability of its air? That depends on who you ask. At a news conference last Tuesday to mark Labor Secretary Marty Walsh’s first visit to the port complex, Port of Los Angeles Executive Director Gene Seroka pointed to the drop in ships at anchor as a sign of progress. “Since we instituted a penalty for long-aging containers, the number of ships at anchor has decreased by more than 40 percent over a four-week period,” Seroka said. The implication had some supply chain watchers blowing their stacks. The …