She is down there so that if any of the others decide to check if the station is really flooded she can kill them, then radio back to Ben and he claims that he/she died swimming to this "Hatch".
She is down there to maintain the machines ensuring all transmissions from the island are blocked (Juliet said this is one of the functions of The Looking Glass).
Bonnie and Greta might be the competing camp of Others that the producers have referenced on podcasts.
They are the surviving members of The DHARMA Initiative, and they look young for the same reason Richard Alpert still looks young. Possibly, they were born on the island.
Extremely unlikely as they seem too young to have been born pre-Incident.
With Sawyer's file written in French for Locke to read, their alleged assignment in Canada, and even suggesting that they were located near Portland, it seems the writers are suggesting that the island is closer than we think. The island's close proximity might also make it more understandable how they are able to interact with the real world, ie Richard and Ethan's travels.