404 on term taxonomy archive pagination only with some terms

Question

On my site I've created a CPT with a hierarchical custom taxonomy:

// **CPT Args**
$args = [
    'labels'             => $labels,
    'public'             => true,
    'publicly_queryable' => false,
    'show_ui'            => true,
    'show_in_menu'       => true,
    'query_var'          => true,
    'rewrite'            => ['slug' => 'documento'],
    'taxonomies'         => ['tipologia'],
    'capability_type'    => 'post',
    'has_archive'        => true,
    'hierarchical'       => false,
    'menu_position'      => null,
    'supports'           => ['title']
];

//**Taxonomy Args**
$args = [
    'hierarchical'      => true,
    'labels'            => $labels,
    'show_ui'           => true,
    'show_admin_column' => true,
    'rewrite'           => ['slug' => 'documenti'
    ],
];

Here the code for pagination:

echo paginate_links(
        [
            'base'    => str_replace( $big, '%#%', esc_url( get_pagenum_link( $big ) ) ),
            'format'  => '?paged=%#%',
            'current' => max( 1, get_query_var( 'paged' ) ),
            'total'   => $wp_query->max_num_pages
        ]
    );

The strange issue is that the pagination works well with some terms:
Example:

documenti/altri-documenti/comunicati/cs-2015/page/2/ <- it works (it doesn't have child terms)
documenti/altri-documenti/comunicati/page/2/ <- not works (this term have children) return 404
documenti/altri-documenti/memore/page/2/ <- it works (this term have children)
documenti/altri-documenti/memore/page/3/ <- not works (this term have children) return 404
documenti/formulari-moduli/page/2/ <- it works (it doesn't have child terms)

It seems like the issue is only with parent terms and not with the last child term.

EDIT

The issue is also with permalinks disabled:

/?tipologia=altri-documenti&paged=2 <- this does not work

Answer 1

user2660802 reports that the problem has been resolved thanks to using Pieter Goosen's suggestion of using pre_get_posts instead of query_posts().

query_posts() breaks the main query, it is slow, and totally stuffs up pagination.