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Consulta MySQL - optimizada

SELECT COUNT(DISTINCT u.id) AS COUNT_QUES FROM urls u
INNER JOIN logs l
ON u.id=l.url_id
WHERE u.url NOT IN (SELECT A.url FROM 
(SELECT * FROM urls u
WHERE SUBSTR(u.url,1,3)!='www')A,
(SELECT * FROM urls v
WHERE SUBSTR(v.url,1,3)='www')B
WHERE A.url=SUBSTR(B.url,5,LENGTH(B.url))
) 
AND l.group_type BETWEEN 4 AND 6
AND u.id NOT IN
(SELECT DISTINCT u.id FROM urls u
INNER JOIN logs l
ON u.id=l.url_id
WHERE u.url NOT IN (SELECT A.url FROM 
(SELECT * FROM urls u
WHERE SUBSTR(u.url,1,3)!='www')A,
(SELECT * FROM urls v
WHERE SUBSTR(v.url,1,3)='www')B
WHERE A.url=SUBSTR(B.url,5,LENGTH(B.url))
) 
AND l.group_type < 4
)

O

SELECT COUNT(DISTINCT CASE WHEN B.URL_ID IS NOT NULL AND FLAG1 = 1 AND FLAG2 = 0 THEN TRIM(LEADING 'www.' FROM A.URL) END)
FROM URLS A 
LEFT JOIN (SELECT URL_ID,
           MAX(CASE WHEN GROUP_TYPE BETWEEN 4 AND 6 THEN 1 ELSE 0 END) FLAG1,
           MAX(CASE WHEN GROUP_TYPE < 4 THEN 1 ELSE 0 END) FLAG2
           FROM LOGS
           GROUP BY URL_ID) B
           ON A.ID = B.URL_ID

Espero que esto funcione para usted. Verifique esto en SQLFIDDLE - http://sqlfiddle.com/#! 2/1fde2/39