Perhaps you should add something to the null columns to make them unique and group on that? I was looking for some sort of sequence to use instead of UUID() but this might work just as well.
SELECT `table1`.*,
IFNULL(ancestor,UUID()) as unq_ancestor
GROUP_CONCAT(id SEPARATOR ',') AS `children_ids`
FROM `table1`
WHERE (enabled = 1)
GROUP BY unq_ancestor