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MySQL adicionando junção diminui a consulta inteira


Você pode tentar desta forma? 
SELECT  SQL_NO_CACHE journey.code, journey.departure, journey.end,
  (select group_concat(pattern_road.latitude) from  pattern_road where pattern_road.section = pattern.section) AS road,
  (select group_concat(link.stop) from link where link.section = pattern.section) AS stop
FROM journey
INNER JOIN journey_day ON journey_day.journey = journey.code
INNER JOIN pattern ON pattern.code = journey.pattern
WHERE journey_day.day = 5 AND TIME(NOW()) BETWEEN journey.departure AND journey.end
GROUP BY journey.code