Charlie bun used to shake his head when he needed his ears cleaned - he used to get a waxy build up. Darwin also does it but he does it when he's excited, just before he starts to binky. So, really it could be either way.
See if you can have a look in her ear - I find shining a little torch in there helps. If you can't see anything, and she's not scratching at her ears then its probably nothing to worry about.