не совсем понятен вопрос, поле updated_at до удаления null или содержит значение?
SELECT DATE_FORMAT(`created_at`, '%y-%m-%d') as`created_at`,
SUM(CASE WHEN updated_at is null THEN 1 ELSE 0 END) AS "created_at_count",
SUM(CASE WHEN updated_at is not null THEN 1 ELSE 0 END) AS "updated_at_count"
FROM `table`
GROUP BY DATE_FORMAT(`created_at`, '%y-%m-%d')
или так:
SELECT DATE_FORMAT(`created_at`, '%y-%m-%d') as`created_at`,
SUM(1) AS "created_at_count",
SUM(CASE WHEN updated_at is not null THEN 1 ELSE 0 END) AS "updated_at_count"
FROM `table`
GROUP BY DATE_FORMAT(`created_at`, '%y-%m-%d')