Conventional meaning of (你)耳朵生翅膀(了)
It's saying fly away, of course.

Chinese also contains similar expressions such as: 长(了)腿 (grew legs) or 长(了)脚  (grew feet) to mean 跑了 (ran away) like:


垃圾总是不翼而飞,难道自己长了脚?
垃圾跑进墙缝中 难道长了脚?
难道鞋子长脚了吗? 


I would imagine the author was going for the same idea here and is just substituting 生翅膀 for 长脚 (because ears can't exactly 'run away'(?), if that makes any sense at all...)