BG, don't worry, it will not affect your employment prospects at EK.
The family medical scheme is basically the same as any other insurance, in as much as if there is a pre-existing condition, it will not be covered (which I guess is fair enough?).
The entire recruitment process is aimed at YOU the candidate and there is no requirement for you to state any family medical issues, however even if you did, it would not affect anything. You would just be made aware that you would be responsible for the costs relating to her illness.
Hope this helps?
Good luck