website with pretty permalinks except pagination

WP permalink handling is sort of layered. They underlying “ugly” permalinks capture the actual logic of the system and the “pretty” permalinks are just cosmetic enhancement on top of it.

Even when pretty permalinks are enabled, the original ugly permalinks still continue to work. But under normal circumstances they get redirected to a pretty version.

You could selectively kill pretty redirect with something like this:

add_filter( 'redirect_canonical', function ( $redirect_url ) {

    if ( is_paged() ) {
        return false;
    }

    return $redirect_url;
}, 10, 1 );

Though this won’t affect how links are generated, so API functions which deal with pagination and stuff will still output pretty results. It’s probably quite involved to override this comprehensively.