The windows in Ten Forward have a direct impact with the planetary surface, both rock and trees as the saucer slides across the landscape. when the saucer comes to a rest we have a close up view of the windows and they are fine- a bit dirty but unbroken.
The windows above Dr. Crusher (and the bridge dome) shattered without anything coming into contact with them. If something had struck them some part of it should have entered the hull as well I would think.
(I also wonder why the good doctor took refuge in a part of the ship which was dangerous- with all that massive interior there was plenty of room in the interior, away from the edges of the hull- IIRC Sickbay itsely was pretty much buried safely inside.
Back to Sisko- I got the feeling his family was with him on that assignment. Jennifer could have been a crewmember and just off duty or a scientist, we never heard. With both parents on a ship it would make sense for their kid to be there as well. The Saratoga may not have been considered a fighting ship- instead of the roll bar weapons pod it had two outrigger sensor dishes. I think Starfleet issued all ships order, regardless of who or what they were. The stupid thing is that they attacked as they arrived instead of waiting for more number and then all attacking at once.