There are several possibilities to detect if the rabbits are in or still out:

1. light barrier at the entrance with a counter
2. gesture sensors which detect direction of movement
3. presence sensors
4. image recognition

I doubt that 1. would reliably work, even when using more than one to determine direction. The gesture sensors are most promising and I'll try the first. The other options are far more complex and a order of magnitude more expensive but should reliably detect how many rabbits are in the hutch.