Would having done ballet from an early age to adulthood permanantly affect the structure of my feet even if retired now?

Yes it could have: Especially if the ballet involved being "on-toe" for many years. This can cause contractures of the toes which are called hammertoes. This can also lead to increased pressure under the metatarsal heads which create the ball of the foot and can cause pain with walking.

Bones: Bones of the body continuously are remodeling along lines of stress. Our activity will effect that remodeling. So yes can be effected need to see podiatrist for evaluation and asses for corrective measures to ease your discomfort. I hope this was helpful.