First, I would close the pop door at night if it were me. Even with my girls in a tightly enclosed run and later inside e-netting, I still close pop doors.
Maybe for whatever reason it went for the eggs only, could be a juvenile, hard to say. What I would be positive about is, it will be back.
Chickens might not be scared because they were undisturbed while eggs were taken. It it did lift the nest box and a buddy pulled eggs out, they wouldn't spook the chickens either.
Regardless of all that, I see two options:
1) Close every hole you can fit your hand into.
2) Close the pop door every night and add a HASP to the nest box lid.
I would do both, but #2 seems more predator proof if you only choose one. Maybe there are 3-10 other options too