If you can't check guests in during the middle of the night then make sure your profile says "no check ins past ___PM" or until whatever time you are able to stay up.
Some guests do have travel plans that change at the last minute. But if they read your policy up front and then still go book a red eye and you can't accommodate the arrival time, then I honestly would say they are out of luck.
I stopped booking a repeat guest who would not respect my time frame. I asked the person to always keep up communication about travel schedule and arrival time. I was always assured a certain time of arrive but that never happened and it always left me waiting up late for hours. So I stopped booking that guest altogether.
But be very frank up front. If you worry that it may limit your booking inquiries from those that can't change their travel plans perhaps you can engage a friend that could assist you in doing a late check in for you. I once paid a friend for checking in someone while I was out of town.