SQL query to count with subtraction from count of other sql table
This works for your sample data, but may need further testing (and possible adjustments) against a larger set of data.

--Demo setup
declare @Table1 table (Id_tag int, BoxNo varchar(5))
declare @Table2 table (DeleteID_tag int, Col1 varchar(5))

insert into @Table1(Id_tag,BoxNo) values
(5699,'A4'),
(5538,'A4'),
(4567,'A5'),
(2222,'A3'),
(1234,'A4');
Insert into @Table2(DeleteID_tag,Col1) values
(1234,'abc'),
(2222,'jkl')
;

--The actual query
SELECT t1.BoxNo
    ,count(*)
FROM @Table1 t1
WHERE NOT EXISTS (
        SELECT *
        FROM @Table2
        WHERE DeleteID_tag = t1.Id_tag
        )
GROUP BY t1.BoxNo




| BoxNo | (No column name) |
|-------|------------------|
| A4    | 2                |
| A5    | 1                |