Quoting bbc.co.uk
See what you think:
Mum to kid eating - Have you finished?
Teacher to student - Have you finished?
Some people would argue that using the present perfect tense and forming the question ‘Have you finished?’ seems to politely give the possibility of more time to finish, whereas 'Are you finished?’ lets the person know they are nearly out of time and no more is available.
Well, personally, I think tone of voice is the all important aspect here. You can express impatience or politeness just from the manner in which you say either of these questions:
Have you finished? Are you finished? (that was my impatient voice)
Have you finished? Are you finished? (that was my polite voice)
Well I hope you could hear the differences there and that you are successful sounding polite or impatient depending on the situation that you’re in!
Source: bbc.co.uk
So it all depends on whether you want to be polite or whether you want to emphasize the fact that time has run out.