Let's begin by confirming your first assumption: you're correct that defunct would not be used to refer to a person, though the dictionary definition might make you think otherwise:
de·funct adj.
Having ceased to exist or live: a defunct political organization.
Though the definition sounds like it could describe a person, you'll note that the example sentence refers to a non-living entity, and I can't imagine native speakers using defunct to describe a person except in a satirical sense.
Now, as for deceased and departed (and your verb tenses). Deceased is definitely appropriate to be used with people. However it is a state of being, not an action, so you would say:
Is your sister deceased?
What you're asking is is your sister currently in the state of being deceased. If you used has you would be saying has your sister deceased recently? and we don't talk like that; you could say has your sister died recently, but we don't use deceased as a verb like that.
[As an interesting aside, while we don't use decease in that manner, we do use predecease (meaning to die before someone else that way). For example, Mary predeceased her older brothers, Jim and Harry.]
Now, as for departed. Departed can be used in the context of people's deaths, but not in the sentence you've got there. If I heard:
Has your sister departed?
I'd wonder if she'd left for the train station yet, and if I heard:
Is your sister departed?
I'd have no idea what was meant.
The way we use departed in this frame of reference is in common phrases, such as the dearly departed. This has the clear meaning of loved ones who have passed away to native speakers.
However in conversation we tend to use euphemisms to avoid touchy subjects, so probably the most common and socially acceptable sentence would be:
Has your sister passed away?