date_query not returning some posts in date range

Your syntax is incorrect for your date_query. It should be an array of an array, not just an array.

I also suspect that your problem might be related to PHP and not WordPress.

Your before date is invalid. PHP only supports dates between 13 December 1901 and 19 January 2038, so your dates need to between those two dates. For reference, see date

You would also want to include the ‘inclusive’ parameter and set it to true for exact matches

Your query should be something like

$args = array(
'post_type' => 'post',
'date_query' => array(
    array(
        'after' => '1980-01-01',
        'before' => '2038-01-01',
        'inclusive' => true,
    ),
),
'cat' => 41,
'fields' => 'ids',
);