"Haven �t done your homework yet?" means "I really don �t want to embarrass you by asking directly because you might not have done it and then I �ll have to get upset with you and I want to avoid confrontation. If I say it this way you will agree with me and I won �t look like a nasty teacher."
My students get very confused with the answers for these implied negative tag questions but they really are extremely common, especially in situations where the speaker is not 100% sure of their circumstances.
The problem for poor students is that as a native speaker I find that we pepper our conversations all the time with these kind of statements to be polite.
eg "You �re not going to the party, are you?" meaning "I hope you are but I don �t want to make a fool of myself in case you think the party is not cool." "I want to fit in with the crowd."
"You �re not going out with Bob, are you?"
"You don �t drink beer, do you?"
Confused?
I �m not surprised!!!!!