você tem que usar colchetes na sub-consulta.
query = "INSERT INTO empallowance(emp_id_fk,allowance_id_fk) VALUES((SELECT emp_id FROM employee WHERE emp_cnic='" + cnic + "'),@allowance_id_fk)";
query = "INSERT INTO empallowance(emp_id_fk,allowance_id_fk) VALUES((SELECT emp_id FROM employee WHERE emp_cnic='" + cnic + "'),@allowance_id_fk)";