How do I remove the entire Media section from the main WordPress navigation without just hiding it?

You are indeed correct, before the admin update(i imagine the UI redesign, etc), unsetting items from the menus would in effect prevent access to those pages, that’s clearly changed now and requires additional cap checking.

This isn’t something i’ve looked into myself(as i’ve just found out this moment), so i can’t speak about methods for doing so.. but it does bother me they’ve now turned a simple unsetting task into a bigger one that requires conditionalised capability checking(it’s just more leg work that was not previously required).

Moving on from the revelation:

Ok, seeing as the remove_menu_page and submenu equivalents are pretty much pointless now(i mean seriously, what good is making a page simply hidden from view) what i’d suggest is looping over the media submenu items and updating the required caps on the fly(if that’s what you need to do).

This appears to have the desired outcome… 🙂

add_action( 'admin_menu', 'remove_menu_links' );
function remove_menu_links() {
    global $submenu;
    remove_menu_page('upload.php');
    foreach( $submenu['upload.php'] as $position => $data ) {
        $submenu['upload.php'][$position][1] = 'desired cap here';
    }
}

NOTE: If you want the items completely gone / inaccessible, simply use a non-existant cap(or just leave the code as it is above)..

Updated version of the above code:

Following on your last comment, perhaps it might be smart to do it like this… or something along these lines..

add_action( 'admin_menu', 'remove_menu_links' );
function remove_menu_links() {
    global $submenu;

    // Remove media for non-admins
    if( !current_user_can('manage_options') )
        remove_menu_page('upload.php');

    // Still need to update cap requirements even when hidden
    foreach( $submenu['upload.php'] as $position => $data ) {
        $submenu['upload.php'][$position][1] = 'manage_options';
    }
}

I realise now you do actually still need the current_user_can call, just to deal with conditionalising the removal of the parent item..

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