The optimization process and recommendations:

1. Avoid Subqueries In From Clause (modified query below): The database cannot properly optimize subqueries in the FROM clause. Therefore, we recommend to extract the subqueries to temporary tables, index them and join to them in the outer query.
2. Create Optimal Indexes (modified query below): The recommended indexes are an integral part of this optimization effort and should be created before testing the execution duration of the optimized query.
3. Use Numeric Column Types For Numeric Values (query line: 32): Referencing a numeric value (e.g. 011) as a string in a WHERE clause might result in poor performance. Possible impacts of storing numbers as varchars: more space will be used, you won't be able to perform arithmetic operations, the data won't be self-validated, aggregation functions like SUM won't work, the output may sort incorrectly and more. If the column is numeric, remove the quotes from the constant value, to make sure a numeric comparison is done.

Optimal indexes for this query:

ALTER TABLE `CUSTINVOICEJOUR` ADD INDEX `custinvoicejour_idx_dataareaid_invoicedate` (`DATAAREAID`,`INVOICEDATE`);
ALTER TABLE `CUSTTRANS` ADD INDEX `custtrans_idx_dataare_invoice_account_transda` (`DATAAREAID`,`INVOICE`,`ACCOUNTNUM`,`TRANSDATE`);
ALTER TABLE `es_temp1` ADD INDEX `es_temp1_idx_dataareaid_refrecid_accountnum` (`DATAAREAID`,`REFRECID`,`ACCOUNTNUM`);
ALTER TABLE `es_temp2` ADD INDEX `es_temp2_idx_dataare_transre_account_transco` (`DATAAREAID`,`TRANSRECID`,`ACCOUNTNUM`,`TRANSCOMPANY`);

The optimized query:

SELECT
        J.INVOICEID,
        T.AMOUNTCUR,
        T.RECID,
        T.ACCOUNTNUM,
        CASE 
            WHEN O.DATAAREAID IS NULL THEN 0 
            ELSE 1 END hasOpenTrans,
CASE 
    WHEN P.DATAAREAID IS NULL THEN 0 
    ELSE 1 END hasPayment 
FROM
CUSTINVOICEJOUR J 
LEFT JOIN
CUSTTRANS T 
    ON T.DATAAREAID = J.DATAAREAID 
    AND T.INVOICE = J.INVOICEID 
    AND T.ACCOUNTNUM = J.INVOICEACCOUNT 
    AND T.TRANSDATE = J.INVOICEDATE 
LEFT JOIN
es_temp1 O 
    ON O.DATAAREAID = T.DATAAREAID 
    AND O.REFRECID = T.RECID 
    AND O.ACCOUNTNUM = T.ACCOUNTNUM 
LEFT JOIN
es_temp2 P 
    ON P.DATAAREAID = T.DATAAREAID 
    AND P.TRANSRECID = T.RECID 
    AND P.ACCOUNTNUM = T.ACCOUNTNUM 
    AND P.TRANSCOMPANY = T.DATAAREAID 
WHERE
J.DATAAREAID = '011' 
AND J.INVOICEDATE >= '2014-06-01'