Using Java 8 APIs,
List empNoList = Arrays.asList(1234, 7678, 2432, 9756556, 3354646);
List parameters = new ArrayList<>();
empNoList.forEach(empNo -> parameters.add("?")); //Use forEach to add required no. of '?'
String commaSepParameters = String.join(",", parameters); //Use String to join '?' with ','
StringBuilder selectQuery = new StringBuilder().append("SELECT COUNT(EMP_ID) FROM EMPLOYEE WHERE EMP_ID IN (").append(commaSepParameters).append(")");