I think for the english translation it would be are you well not are you healthy it doesnt seem natural to ask are you healthy.
No, there is a difference.
Jste zdravá? = 'Are you healthy?' A doctor might ask you this one when he's taking your medical history.
Je vám dobře? = 'Are you (feeling) well?' You see a pale old lady staggering in the supermarket and you want to inquire if she's feeling ok or if she needs help.