Obviously it’s your MySQL server that can’t handle it. Needs way more horsepower...

# User@Host: cgkiwigo[cgkiwigo] @ localhost []  Id:   493
# Query_time: 68.482646  Lock_time: 0.000047 Rows_sent: 0  Rows_examined: 2830964
SET timestamp=1533946952;
SELECT DISTINCT(id)
  FROM piwigo_images INNER JOIN piwigo_image_category ON id=image_id
  WHERE category_id NOT IN (0)
    AND level>0;
# User@Host: cgkiwigo[cgkiwigo] @ localhost []  Id:   488
# Query_time: 6.529592  Lock_time: 0.000083 Rows_sent: 1  Rows_examined: 1415482
SET timestamp=1533946952;
SELECT COUNT(DISTINCT(image_id)) as total
  FROM piwigo_image_category
  WHERE category_id NOT IN (0)
    AND image_id NOT IN (0);
# User@Host: cgkiwigo[cgkiwigo] @ localhost []  Id:   492
# Query_time: 68.824714  Lock_time: 0.000048 Rows_sent: 0  Rows_examined: 2830964
SET timestamp=1533946952;
SELECT DISTINCT(id)
  FROM piwigo_images INNER JOIN piwigo_image_category ON id=image_id
  WHERE category_id NOT IN (0)
    AND level>0;
# Time: 180810 17:22:33
# User@Host: cgkiwigo[cgkiwigo] @ localhost []  Id:   494
# Query_time: 68.708064  Lock_time: 0.000047 Rows_sent: 0  Rows_examined: 2830964
SET timestamp=1533946953;
SELECT DISTINCT(id)
  FROM piwigo_images INNER JOIN piwigo_image_category ON id=image_id
  WHERE category_id NOT IN (0)
    AND level>0;