How to remove or add submenu item on plugin activate or deactive

If you want to add items dynamically at every page call, you can look this answer :
Dynamically add sub-categories to any category in the menu

And to add an element directly, you can try that for a custom link e.g. :

// create the new element

$post = [
    'post_title' => "StackExchange " . date("H:i:s"),
    "menu_order" => 700, // position in the menu
    'post_type' => 'nav_menu_item',
    'post_status' => 'publish',
];

$menu_item_db_id = wp_insert_post( $post );

update_post_meta( $menu_item_db_id, 'url', "https://wordpress.stackexchange.com/");
update_post_meta( $menu_item_db_id, 'type', "custom");
update_post_meta( $menu_item_db_id, '_menu_item_menu_item_parent', 0); // change to create a sub menu


// association to the menu

$menuLocations = get_nav_menu_locations();
$menuID = (int) $menuLocations['primary'];

wp_set_object_terms($menu_item_db_id, $menuID, "nav_menu");