Retriving array size from serialized data

Your Query is wrong beacuse your are searching for the user_id inside the meta_value column instead of the user_id column.
In this case i see no point in creating a custom query just for that, So here is how you can do it using the native function get_user_meta

$data = get_user_meta( get_current_user_id(), 'bookmark_posts' );
$number = count($data);
if( $number > 0 ){
    echo 'Total bookmarks ('.$number.')';
}