Checking if String has unique values
In this case I would go the regex route. Your code is basically saying: Anything that parses as a digit is fine, just so long as everything is a digit, and at least one of them is not zero.

Express that as a regular expression:

private static final Pattern validEmployeeNumber = Pattern.compile("^[0-9]*[1-9][0-9]*$");


Then your function becomes:

private static final Pattern validEmployeeNumber = Pattern.compile("^[0-9]*[1-9][0-9]*$");

private static boolean employeeNumberCheck(String employeeNumber){
    return validEmployeeNumber.matcher(employeeNumber).matches();
}   


See it running in ideone