I dunno I only ran through it once.
First time I never met Aurora and let the bomb explode, but I never did Anno's mission to turn on the shields...
Everything was intact, even Aurora's shop.
There may be multiple factors at play here, like whether or not you met Aurora and/or Anno, if you're still in the wild when the bomb goes off.
Aurora seems to survive with her shop no matter what if you blow up the planet before meeting her.
I'll run through the quest a few more times to make sure.
Alright:
If you only beat Tam and leave after being notified about the bomb:
Tam informs you it was just a bluff, the Captain thanks you for not killing Tam, and they said they would set off the bomb if I went to fight the rest of them. Oh and fuck me for taking Tam-Wolf from her and I'm lucky she had a spare or she'd be super pissed at me. Oh, and she thinks we should should each other again sometime.
Did not meet Anno or Aurora and beat one of the other members.
Bomb goes off, Aurora is nowhere to be seen. Her shop is gone. Aurora is not mentioned at all.