Is there one door that multiple chickens walk through, or is it one door per chicken? Personally, I would put a sonar sensor over ONE chicken nest. If the distance is large, there's no chicken sitting there. If the distance is small, there IS a chicken sitting there. I'm fairly new to Arduino and I've never used RFID, so that's how I would handle it using what I know. It seems like if there's only one door, you would need an RFID solution that worked 100% of the time or else your Arduino might think that a chicken is inside the coup when it really isn't, causing you to reboot the program or go in and fix it.