Hermione never told her parents she was living with a young criminal and his mother. She simply told them she was at the Weasleys. And the Weasleys thought she was at her parents. She did, however, tell the mail owl to deliver her parcels and letters to the safe house. 

So on that fateful day when the death eaters came to the safe house, she didn't know where to take Draco and Narcissa. Both the Weasley and Granger families would be in danger. But then she realized the second safehouse currently occupied by only two beings.

"Draco, Narcissa, grab my arm. We are going somewhere." Hermione took one last look at her little home, grabbed her purple bag, and apparated. "Welcome to Grimmauld place. I don't know if either of you has been here before but this is the safest safe house there is." Hermione said. 

"PANSY, get your arse down here and say hello. KREACHER, you too!" Hermione yelled for her girlfriend and house elf. Draco just looked a bit taken aback and stared at Hermione in shock. "What? Are you surprised that I live here or that I'm dating your ex-girlfriend?" Hermione just shrugged and walked into the kitchen. Draco and Narcissa trailed behind her. There was some soupy substance in a pot cooking on the stove.