Thousands of thumbnails in one directory might slow down file requests. I made a simple modification to video_embed_field_field_presave (video_embed_field.field.inc) to prevent this.

I added a prefix to the local path to group the files by creation date.

$prefix=date('Ymd', $entity->created );
$local_path = "public://video_embed_field_thumbnails/{$info['handler']}/$prefix/{$info['id']}.$thumb_extension";

Less complicated than adding support for filefield_paths (https://www.drupal.org/project/filefield_paths).

Might be usefull for these issues:
https://www.drupal.org/node/1844782
https://www.drupal.org/node/2525796

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DrupalThomas created an issue.