A federal judge threw out the U.S. Customs Service's employee drug testing program in a decision that a lawyer said may indicate whether President Reagan's program will hold up in court. U.S. District Judge Robert F. Collins ruled in New Orleans that the customs program was unconstitutional because it constituted illegal and unwarranted search and seizure. Lois Williams, a lawyer for the National Treasury Employees Union, said the ruling would have far-reaching effects on the President's order for mandatory testing of federal employees. "We believe . . . there is no way the executive order can go on," she said.