Join query is slow.

N1QL
1 
SELECT RAW a.number
FROM `my_bk` AS a
LEFT JOIN `my_bk` AS b ON meta(a).id = b.check_id AND b.type = 'bbb'
WHERE
  a.type = 'aaa' AND
  a.name = 'name' AND
  a.class = 1 AND b IS MISSING

Select number that exists in A and does not exist in B.

Each row is about 100,000.

2

What indices do you have defined ?

ADVISE suggests:

CREATE INDEX adv_name_type_class_number ON `my_bk`(`name`,`type`,`class`,`number`);
CREATE INDEX adv_type_check_id ON `my_bk`(`type`,`check_id`);
3

Also:

WITH b AS (SELECT check_id FROM `my_bk` b1 WHERE type = 'bbb')                                                            
SELECT a.`number`
FROM `my_bk` a LEFT OUTER JOIN b ON meta(a).id = b.check_id
WHERE a.type = 'aaa'
AND a.name = 'name'
AND a.class = 1
AND b IS MISSING
;

Or:

WITH b AS (SELECT check_id FROM `my_bk` b1 WHERE type = 'bbb')                                                    
SELECT a.`number`
FROM `my_bk` a
WHERE a.type = 'aaa'
AND a.name = 'name'
AND a.class = 1
AND meta(a).id NOT IN (SELECT RAW b.check_id FROM b b2)
;

may offer different performance.

HTH.

4

Same lines of @dh ,

CREATE INDEX ix1 ON `my_bk`(`name`,`class`,`number`) WHERE type = "aaa";
CREATE INDEX ix2 ON `my_bk`(`check_id`) WHERE type = "bbb";

The following uses covering index as b is whole document not used any where.
In Join cases see if you can use HASH JOIN hints described in Example 9 ANSI JOIN Support in N1QL - The Couchbase Blog

SELECT d.`number`
FROM ( SELECT a.`number`, b.check_id
       FROM `my_bk` a
       LEFT OUTER JOIN b ON meta(a).id = b.check_id AND b.type = "bbb"
       WHERE a.type = 'aaa'
       AND a.name = 'name'
       AND a.class = 1) AS d
WHERE d.check_id IS MISSING ;

OR

WITH b AS (SELECT DISTINCT RAW check_id FROM `my_bk` b1 WHERE type = 'bbb')
SELECT a.`number`
FROM `my_bk` a
WHERE a.type = 'aaa' AND a.name = 'name' AND a.class = 1 AND meta(a).id NOT IN b;

OR

The following two are same (except syntax) see any faster. NOTE: Output as ARRAY.

SELECT RAW ARRAY_AGG(CASE WHEN b.check_id IS MISSING THEN a.`number` END)
FROM `my_bk` a
LEFT OUTER JOIN b ON meta(a).id = b.check_id AND b.type = "bbb"
WHERE a.type = 'aaa' AND a.name = 'name' AND a.class = 1;

OR

SELECT RAW ARRAY_AGG(a.`number`) FILTER (WHERE b.check_id IS MISSING)
FROM `my_bk` a
LEFT OUTER JOIN b ON meta(a).id = b.check_id AND b.type = "bbb"
WHERE a.type = 'aaa' AND a.name = 'name' AND a.class = 1;
5

CREATE INDEX adv_name_type_class_number ON my_bk(name,class,number) WHERE (type=“aaa”);
CREATE INDEX adv_type_check_id ON my_bk(check_id) WHERE (type=“bbb”);